fa

基因组文件，记录每条染色体或者contig的序列信息
samtools faidx 后面跟fa文件，可以对其进行建立fai文件及基因的索引文件

>1 dna:chromosome chromosome:AGPv4:1:1:307041717:1 REF
TTTTCGACAAAAATGGGGTTGTGTGGCCATTGATCATCGACCAGAGGCTCATACACCTCA
CCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCT
TGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGTTCATGGCTAT
TTTCGACAAAAATGGGGGTTGTGTGGCCATTGATCATCGACCAGAGCTCATACACCTCAC
CCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTT
GGTCAAAAATCCGTAGGTGTTAGCCTTCGTATTATTGAAAATGGTCGTTCATGGCTATTT
TCGACAAAAATGGGGGTTGTGTGGCCATTGATCATCGACCAGAGGCTCATACACCTCACC
CCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTG
GTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGTTCATGGCTATTT
TCGACAAAATGGGGGTTGTGTGGCCATTGATCATCGACCAGAGGCTCATACACCTCACCC

fai

基因组的索引文件

1    307041717   55  60  61
2   244442276   312159189   60  61
3   235667834   560675558   60  61
4   246994605   800271245   60  61
5   223902240   1051382482  60  61
6   174033170   1279016481  60  61
7   182381542   1455950259  60  61
8   181122637   1641371549  60  61
9   159769782   1825512952  60  61
10  150982314   1987945621  60  61
...

gff

基因组注释文件


##gff-version   3
##sequence-region   1 1 249250621
##sequence-region   10 1 135534747
##sequence-region   11 1 135006516
##sequence-region   12 1 133851895
##sequence-region   13 1 115169878
##sequence-region   14 1 107349540
##sequence-region   15 1 102531392
##sequence-region   16 1 90354753
##sequence-region   17 1 81195210
##sequence-region   18 1 78077248
##sequence-region   19 1 59128983
##sequence-region   2 1 243199373
##sequence-region   20 1 63025520
##sequence-region   21 1 48129895
##sequence-region   22 1 51304566
##sequence-region   3 1 198022430
##sequence-region   4 1 191154276
##sequence-region   5 1 180915260
##sequence-region   6 1 171115067
##sequence-region   7 1 159138663
##sequence-region   8 1 146364022
##sequence-region   9 1 141213431
##sequence-region   GL000191.1 1 106433
##sequence-region   MT 1 16569
##sequence-region   X 1 155270560
##sequence-region   Y 2649521 59034049
#!genome-build  GRCh37.p13
#!genome-version GRCh37
#!genome-date 2009-02
#!genome-build-accession NCBI:GCA_000001405.14
#!genebuild-last-updated 2013-09
1   GRCh37  chromosome  1   249250621   .   .   .   ID=chromosome:1;Alias=CM000663.1,NC_000001.10
###
1   cpg biological_region   10469   11240   1.3e+03    .   .   external_name=oe %3D 0.79;logic_name=cpg
1   Eponine biological_region   10650   10657   0.999   +  .   logic_name=eponine
1   Eponine biological_region   10656   10658   0.999   -   .   logic_name=eponine
1   Eponine biological_region   10678   10687   0.999   +  .   logic_name=eponine
1   Eponine biological_region   10682   10689   0.999   -   .   logic_name=eponine
1   Eponine biological_region   10707   10716   0.999   +  .   logic_name=eponine
1   Eponine biological_region   10709   10719   0.999   -   .   logic_name=eponine
1   Eponine biological_region   10736   10748   0.999   -   .   logic_name=eponine
1   ensembl_havana  pseudogene  11869   14412   .   +  .   ID=gene:ENSG00000223972;Name=DDX11L1;biotype=pseudogene;description=DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 [Source:HGNC Symbol%3BAcc:37102];gene_id=ENSG00000223972;logic_name=ensembl_havana_gene;version=4
1   havana  processed_transcript    11869   14409   .   +  .   ID=transcript:ENST00000456328;Parent=gene:ENSG00000223972;Name=DDX11L1-002;biotype=processed_transcript;havana_transcript=OTTHUMT00000362751;havana_version=1;tag=basic;transcript_id=ENST00000456328;version=2
1   havana  exon    11869   12227   .   +  .   Parent=transcript:ENST00000456328;Name=ENSE00002234944;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002234944;rank=1;version=1
1   havana  exon    12613   12721   .   +  .   Parent=transcript:ENST00000456328;Name=ENSE00003582793;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003582793;rank=2;version=1
1   havana  exon    13221   14409   .   +  .   Parent=transcript:ENST00000456328;Name=ENSE00002312635;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002312635;rank=3;version=1
1   ensembl pseudogenic_transcript  11872   14412   .   +  .   ID=transcript:ENST00000515242;Parent=gene:ENSG00000223972;Name=DDX11L1-201;biotype=transcribed_unprocessed_pseudogene;transcript_id=ENST00000515242;version=2
1   ensembl exon    11872   12227   .   +  .   Parent=transcript:ENST00000515242;Name=ENSE00002234632;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=ENSE00002234632;rank=1;version=1
1   ensembl exon    12613   12721   .   +  .   Parent=transcript:ENST00000515242;Name=ENSE00003608237;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=ENSE00003608237;rank=2;version=1
...
1       havana  exon    860260  860328  .       +       .       Parent=transcript:ENST00000420190;Name=ENSE00001637883;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001637883;rank=1;version=1
1       havana  five_prime_UTR  860260  860328  .       +       .       Parent=transcript:ENST00000420190
1       havana  five_prime_UTR  861302  861321  .       +       .       Parent=transcript:ENST00000420190
1       havana  exon    861302  861393  .       +       .       Parent=transcript:ENST00000420190;Name=ENSE00001763717;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=ENSE00001763717;rank=2;version=1
1       havana  CDS     861322  861393  .       +       0       ID=CDS:ENSP00000411579;Parent=transcript:ENST00000420190;protein_id=ENSP00000411579
1       havana  exon    865535  865716  .       +       .       Parent=transcript:ENST00000420190;Name=ENSE00002727207;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=ENSE00002727207;rank=3;version=1
1       havana  CDS     865535  865716  .       +       0       ID=CDS:ENSP00000411579;Parent=transcript:ENST00000420190;protein_id=ENSP00000411579
1       havana  exon    866419  866469  .       +       .       Parent=transcript:ENST00000420190;Name=ENSE00002696520;constitutive=0;ensembl_end_phase=2;ensembl_phase=2;exon_id=ENSE00002696520;rank=4;version=1
1       havana  CDS     866419  866469  .       +       1       ID=CDS:ENSP00000411579;Parent=transcript:ENST00000420190;protein_id=ENSP00000411579
1       havana  exon    871152  871276  .       +       .       Parent=transcript:ENST00000420190;Name=ENSE00002703998;constitutive=0;ensembl_end_phase=1;ensembl_phase=2;exon_id=ENSE00002703998;rank=5;version=1

fastq

存储测序数据结果的文件，记录有序列及其质量信息等

@A00545:25:H77GTDSXX:4:1101:1163:1000 1:N:0:GCAGGCAT+TAAGGCGC
CATCATAGCACAATGCTTTGAATTACAATAAAGAGTAAGTAATAATATTACAAACTAGAGCCATTTACATAATATAAATCAAAGTACACAAAATCGAAACGTAGCCAACGTAAATTAACCCACCACAGACAATAGACTAGGGGAGGTCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFF:FFF:FFFF,FFFFF:FFFFFFFFFFF:FFFFF:FF:FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF
@A00545:25:H77GTDSXX:4:1101:4237:1000 1:N:0:GCAGGCAT+TAAGGCGC
CAAACTTGGTCTTTTTATTGGCTGAGTGTGAACCTTTTACACCTGTATAATCTATACACTTGGGCAAACTAGTTAGTCCAAAGATTTGTGTTGGGCAATTCAACCACCAAAATTATATAGGAACTAGGTGTAAGCCTAATTCCCTTTCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF
@A00545:25:H77GTDSXX:4:1101:4381:1000 1:N:0:GCAGGCAT+TAAGGCGC
ACCTTCAACAAAAGGGTACCTGTACCCGAAACCGACACAGGTGGGTAGGTAGAGAATACCTAGGGGCGCGAGACAACTCTCTCTAAGGAACTCGGCAAAATAGCCCCGTAACTTCGGGAGAAGGGGTGCCCCCTCGCAAAAGGGGGTCGC

bam

测序数据比对基因后的二进制文件
因为是二进制文件，将其打开可读模式可以使用：samtools view bam |less 查看

@HD VN:1.5  SO:coordinate
@SQ    SN:1    LN:307041717
@SQ    SN:2    LN:244442276
@SQ    SN:3    LN:235667834
...
@SQ    SN:B73V4_ctg187 LN:6454
@SQ    SN:B73V4_ctg76  LN:5568
@RG    ID:GWAS_85  SM:GWAS_85  PL:ILLUMINA
@PG    ID:bwa  CL:/usr/local/sentieon-genomics-201808.01/libexec/bwa mem -M -R @RG\tID:GWAS_85\tSM:GWAS_85\tPL:ILLUMINA -t 32 -K 10000000 /annoroad/ref//Zea_mays.B73_RefGen_v4.dna.toplevel.fa /annoroad/input/23153_R1.fq.gz /annoroad/input/23153_R2.fq.gz PN:bwa  VN:0.7.15-r1140
@PG    ID:sentieon-sort    CL:/usr/local/sentieon-genomics-201808.01/libexec/util sort -r /annoroad/ref//Zea_mays.B73_RefGen_v4.dna.toplevel.fa -t 32 --sam2bam -o /annoroad/out/test//GWAS_85.sorted.bam -    PN:sentieon-sort    PP:bwa  VN:sentieon-genomics-201808.01
A00545:25:H77GTDSXX:4:2240:11026:31767  163 1   15  0   150M    =  115 249 GGGGTTGTGTGGCCATTGATCATCAACCAGATGCTCATACACCTCTCCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCATCGGTATAATTGAAAAT  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFF:FFFF:F:FF,::,FFFFFFFFF,FFFFF,FFF:FFF,FFFFFF:F:FFFF::F:,FFFFFFFFFFFFFFFFFFFFF,FFFFF:FFF  NM:i:5  MD:Z:24G6G13A86T7T9 AS:i:125    XS:i:130    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:2426:20518:32268  163 1   22  0   150M    =  404 532 TGTGGCCATTGATCATCGACCAGCGGCTCATACACCACACCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTAGTT  FFFF:F,:F:FFFFFFFFFFFFFF,:,F::F,,F,FFFFFFFFFFFFF::F::F,F,,F:F:F,FFFF:FFF:F,,FFFFFFF,FF,FFFF,FFF,FFFFF,FFFFFFF,,,F:F:F:FFFFF,FFFF,:,:F,FFFF::FF:F,F::FF  NM:i:3  MD:Z:23A12T109C3    AS:i:136    XS:i:136    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:1113:1118:7467    99  1   25  2   150M    =  412 537 GGCCATTGATCATCGACCAGAGGCTCATACACCTCACCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGTTCAT  FFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF::FFFF:,FFFFFFFFFF::FF:FFFFFFFFF:FFFFF:FFFFFFFFF  NM:i:0  MD:Z:150    AS:i:150    XS:i:150    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:2215:13141:24784  163 1   27  0   150M    =  405 527 CCATTGATCATCGACCAGAGGCTCATACACCTCACCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGTTCATGG  F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFF::FFFFFFF:FFFFFFFFF:FFFF,F,FFFFFFFFFFFFFFFFFFFFFFF:F,F,FFF::F:FFF,FFFFF,FFFF:FFFFF,FFF::FF,FFFFF:,  NM:i:0  MD:Z:150    AS:i:150    XS:i:150    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:2235:25084:19852  163 1   36  0   150M    =  139 248 ATCGACCAGAGGCTCATACACCTCACCCCACATATGTTTCCTTGCTATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGTTCATGGCTATTTTCG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFF,F:FFFFFFFFFFF::FFFFFFFFFF,F::FF:FFFFFFFFFFF,FFFFFFFFF:F::F,FFFFFFFFFFFFF:FFF:F:F:FFF:,,:FF:F:FFF  NM:i:1  MD:Z:45C104 AS:i:145    XS:i:145    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:1651:9598:13197   99  1   37  0   150M    =  404 517 TCGACCAGAGGCTCATACACCTCACCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGATCATGGCTATTTTCGG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:::FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF,  NM:i:2  MD:Z:133T15A0   AS:i:144    XS:i:144    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:1503:10285:6590   65  1   38  0   140M10S 9   151394348   0   CGACCAGAGGCTCATACACCTCACCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTGTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGTTCATGGCAATGATCAGC  FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF,,:FFFFFFFFFFFFFFFFFFF,FFFFF,,,,,,,,,,,F  NM:i:1  MD:Z:65C74  AS:i:135    XS:i:135    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:2474:20907:33912  99  1   40  2   150M    =  421 529 ACCAGAGGCTCATACACCTCACCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGTTCATGGCTATTTTCGACAA  FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFF:FFF,:FFFFF,FF,FFFFFFF:FFFFFFFFFFFFFFFF,FFF:FFFFF:FFFFFFFFFFFFF,FFFF:F,FFF:FFF:FFFFFFFF,FFFFFFFFF:FFFFFFFFFF,F:F  NM:i:0  MD:Z:150    AS:i:150    XS:i:150    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:1673:8115:30608   99  1   45  0   143M1D7M    =  409 514 AGGCTCATACACCTCACCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGCCTTCGGTATTATTGAAAATGGTCGTTCATGGCTATTTTCTACAAAATGG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,,FFFFF:FF  NM:i:2  MD:Z:140G2^A7   AS:i:142    XS:i:142    RG:Z:GWAS_85
A00545:25:H77GTDSXX:4:2247:8657:11819   163 1   47  0   98M52S  =  225 275 GCTCATACACCTCACCCCACATATGTTTCCTTGCCATAGATCACATTCTTGGATTTCTGGTGGAGACCATTTCTTGGTCAAAAATCCGTAGGTGTTAGAGCGGACGAGAGTCGTGTATGGACTGTCTGTGATAAACTGTGGAAATATGGG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:,,,:,,,F,,,F,F,,:F,FFFF,F,,,,,F,FF,,,F,,,,:,:,,:,FF  NM:i:0  MD:Z:98 AS:i:98 XS:i:98 RG:Z:GWAS_85
...

vcf

记录变异信息的文件

##fileformat=VCFv4.2
##FILTER=<ID=HighFS,Description="FS >60.0">
##FILTER=<ID=LowDP,Description="DP< 4.0">
##FILTER=<ID=LowQD,Description="QD < 2.0">
##FILTER=<ID=LowQUAL,Description="QUAL < 30.0">
##FILTER=<ID=LowRPRS,Description="ReadPosRankSum < -8.0">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="The phred-scaled genotype likelihoods rounded to the closest integer">
##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.5-0-g36282e4,Date="Sat Mar 30 10:26:28 CST 2019",Epoch=1553912788946,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/annoroad/ref/Zea_mays.B73_RefGen_v4.dna.toplevel.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/annoroad/out/test//ALL.raw.vcf.gz) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/annoroad/out/test/ALL.snp.raw.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,Version=3.5-0-g36282e4,Date="Tue Apr 02 09:16:00 UTC 2019",Epoch=1554196560540,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/nas/data1/bioinfo/PROJECT/Commercial/Cooperation/AP/Resequence/ANYWCR180570/YWCR180570-01/std/zhouna/info/genome/Zea_mays.B73_RefGen_v4.dna.toplevel.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=ERROR log_to_file=null help=false version=false variant=(RodBinding name=variant source=ALL.snp.raw.vcf) mask=(RodBinding name= source=UNBOUND) out=/nas/data1/bioinfo/PROJECT/Commercial/Cooperation/AP/Resequence/ANYWCR180570/YWCR180570-01/std/zhouna/Analysis/Result/SNP_INDEL/ALL.snp.filter1.vcf filterExpression=[QD < 2.0, ReadPosRankSum < -8.0, FS >60.0, QUAL < 30.0, DP< 4.0] filterName=[LowQD, LowRPRS, HighFS, LowQUAL, LowDP] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=true invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Combined depth across samples">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts, for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS mapping quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##SentieonCommandLine.GVCFtyper=<ID=GVCFtyper,Version="sentieon-genomics-201808.01",Date="2019-03-29T12:13:29Z",CommandLine="/usr/local/sentieon-genomics-201808.01/libexec/driver -r /annoroad/ref//Zea_mays.B73_RefGen_v4.dna.toplevel.fa -t 32 --algo GVCFtyper /annoroad/out/test//ALL.raw.vcf.gz GWAS_1.raw.g.vcf.gz GWAS_10.raw.g.vcf.gz GWAS_100.raw.g.vcf.gz GWAS_101.raw.g.vcf.gz GWAS_102.raw.g.vcf.gz GWAS_105.raw.g.vcf.gz GWAS_108.raw.g.vcf.gz GWAS_109.raw.g.vcf.gz GWAS_11.raw.g.vcf.gz GWAS_110.raw.g.vcf.gz GWAS_111.raw.g.vcf.gz GWAS_112.raw.g.vcf.gz GWAS_113.raw.g.vcf.gz GWAS_114.raw.g.vcf.gz GWAS_116.raw.g.vcf.gz GWAS_118.raw.g.vcf.gz GWAS_119.raw.g.vcf.gz GWAS_12.raw.g.vcf.gz GWAS_120.raw.g.vcf.gz GWAS_121.raw.g.vcf.gz GWAS_122.raw.g.vcf.gz GWAS_123.raw.g.vcf.gz GWAS_125.raw.g.vcf.gz GWAS_126.raw.g.vcf.gz GWAS_127.raw.g.vcf.gz GWAS_128.raw.g.vcf.gz GWAS_129.raw.g.vcf.gz GWAS_13.raw.g.vcf.gz GWAS_130.raw.g.vcf.gz GWAS_131.raw.g.vcf.gz GWAS_132.raw.g.vcf.gz GWAS_133.raw.g.vcf.gz GWAS_134.raw.g.vcf.gz GWAS_14.raw.g.vcf.gz GWAS_144.raw.g.vcf.gz GWAS_15.raw.g.vcf.gz GWAS_152.raw.g.vcf.gz GWAS_16.raw.g.vcf.gz GWAS_168.raw.g.vcf.gz GWAS_17.raw.g.vcf.gz GWAS_18.raw.g.vcf.gz GWAS_183.raw.g.vcf.gz GWAS_186.raw.g.vcf.gz GWAS_189.raw.g.vcf.gz GWAS_19.raw.g.vcf.gz GWAS_192.raw.g.vcf.gz GWAS_197.raw.g.vcf.gz GWAS_2.raw.g.vcf.gz GWAS_20.raw.g.vcf.gz GWAS_207.raw.g.vcf.gz GWAS_21.raw.g.vcf.gz GWAS_210.raw.g.vcf.gz GWAS_213.raw.g.vcf.gz GWAS_214.raw.g.vcf.gz GWAS_217.raw.g.vcf.gz GWAS_22.raw.g.vcf.gz GWAS_221.raw.g.vcf.gz GWAS_227.raw.g.vcf.gz GWAS_229.raw.g.vcf.gz GWAS_23.raw.g.vcf.gz GWAS_233.raw.g.vcf.gz GWAS_236.raw.g.vcf.gz GWAS_24.raw.g.vcf.gz GWAS_242.raw.g.vcf.gz GWAS_243.raw.g.vcf.gz GWAS_244.raw.g.vcf.gz GWAS_25.raw.g.vcf.gz GWAS_250.raw.g.vcf.gz GWAS_254.raw.g.vcf.gz GWAS_255.raw.g.vcf.gz GWAS_256.raw.g.vcf.gz GWAS_257.raw.g.vcf.gz GWAS_258.raw.g.vcf.gz GWAS_259.raw.g.vcf.gz GWAS_26.raw.g.vcf.gz GWAS_268.raw.g.vcf.gz GWAS_27.raw.g.vcf.gz GWAS_272.raw.g.vcf.gz GWAS_273.raw.g.vcf.gz GWAS_276.raw.g.vcf.gz GWAS_277.raw.g.vcf.gz GWAS_278.raw.g.vcf.gz GWAS_28.raw.g.vcf.gz GWAS_280.raw.g.vcf.gz GWAS_286.raw.g.vcf.gz GWAS_288.raw.g.vcf.gz GWAS_29.raw.g.vcf.gz GWAS_294.raw.g.vcf.gz GWAS_297.raw.g.vcf.gz GWAS_3.raw.g.vcf.gz GWAS_30.raw.g.vcf.gz GWAS_303.raw.g.vcf.gz GWAS_304.raw.g.vcf.gz GWAS_305.raw.g.vcf.gz GWAS_306.raw.g.vcf.gz GWAS_309.raw.g.vcf.gz GWAS_31.raw.g.vcf.gz GWAS_310.raw.g.vcf.gz GWAS_314.raw.g.vcf.gz GWAS_32.raw.g.vcf.gz GWAS_320.raw.g.vcf.gz GWAS_321.raw.g.vcf.gz GWAS_322.raw.g.vcf.gz GWAS_323.raw.g.vcf.gz GWAS_324.raw.g.vcf.gz GWAS_325.raw.g.vcf.gz GWAS_328.raw.g.vcf.gz GWAS_329.raw.g.vcf.gz GWAS_33.raw.g.vcf.gz GWAS_330.raw.g.vcf.gz GWAS_336.raw.g.vcf.gz GWAS_338.raw.g.vcf.gz GWAS_339.raw.g.vcf.gz GWAS_34.raw.g.vcf.gz GWAS_340.raw.g.vcf.gz GWAS_341.raw.g.vcf.gz GWAS_342.raw.g.vcf.gz GWAS_343.raw.g.vcf.gz GWAS_344.raw.g.vcf.gz GWAS_345.raw.g.vcf.gz GWAS_346.raw.g.vcf.gz GWAS_347.raw.g.vcf.gz GWAS_348.raw.g.vcf.gz GWAS_349.raw.g.vcf.gz GWAS_35.raw.g.vcf.gz GWAS_351.raw.g.vcf.gz GWAS_353.raw.g.vcf.gz GWAS_354.raw.g.vcf.gz GWAS_355.raw.g.vcf.gz GWAS_356.raw.g.vcf.gz GWAS_357.raw.g.vcf.gz GWAS_358.raw.g.vcf.gz GWAS_359.raw.g.vcf.gz GWAS_36.raw.g.vcf.gz GWAS_360.raw.g.vcf.gz GWAS_361.raw.g.vcf.gz GWAS_362.raw.g.vcf.gz GWAS_363.raw.g.vcf.gz GWAS_366.raw.g.vcf.gz GWAS_367.raw.g.vcf.gz GWAS_368.raw.g.vcf.gz GWAS_37.raw.g.vcf.gz GWAS_370.raw.g.vcf.gz GWAS_371.raw.g.vcf.gz GWAS_372.raw.g.vcf.gz GWAS_373.raw.g.vcf.gz GWAS_374.raw.g.vcf.gz GWAS_375.raw.g.vcf.gz GWAS_376.raw.g.vcf.gz GWAS_377.raw.g.vcf.gz GWAS_378.raw.g.vcf.gz GWAS_379.raw.g.vcf.gz GWAS_38.raw.g.vcf.gz GWAS_380.raw.g.vcf.gz GWAS_381.raw.g.vcf.gz GWAS_383.raw.g.vcf.gz GWAS_384.raw.g.vcf.gz GWAS_385.raw.g.vcf.gz GWAS_387.raw.g.vcf.gz GWAS_388.raw.g.vcf.gz GWAS_389.raw.g.vcf.gz GWAS_39.raw.g.vcf.gz GWAS_390.raw.g.vcf.gz GWAS_391.raw.g.vcf.gz GWAS_392.raw.g.vcf.gz GWAS_394.raw.g.vcf.gz GWAS_395.raw.g.vcf.gz GWAS_396.raw.g.vcf.gz GWAS_397.raw.g.vcf.gz GWAS_398.raw.g.vcf.gz GWAS_399.raw.g.vcf.gz GWAS_4.raw.g.vcf.gz GWAS_40.raw.g.vcf.gz GWAS_400.raw.g.vcf.gz GWAS_401.raw.g.vcf.gz GWAS_402.raw.g.vcf.gz GWAS_403.raw.g.vcf.gz GWAS_404.raw.g.vcf.gz GWAS_405.raw.g.vcf.gz GWAS_406.raw.g.vcf.gz GWAS_407.raw.g.vcf.gz GWAS_408.raw.g.vcf.gz GWAS_409.raw.g.vcf.gz GWAS_41.raw.g.vcf.gz GWAS_410.raw.g.vcf.gz GWAS_411.raw.g.vcf.gz GWAS_412.raw.g.vcf.gz GWAS_413.raw.g.vcf.gz GWAS_414.raw.g.vcf.gz GWAS_415.raw.g.vcf.gz GWAS_416.raw.g.vcf.gz GWAS_417.raw.g.vcf.gz GWAS_418.raw.g.vcf.gz GWAS_419.raw.g.vcf.gz GWAS_42.raw.g.vcf.gz GWAS_420.raw.g.vcf.gz GWAS_421.raw.g.vcf.gz GWAS_422.raw.g.vcf.gz GWAS_423.raw.g.vcf.gz GWAS_424.raw.g.vcf.gz GWAS_425.raw.g.vcf.gz GWAS_426.raw.g.vcf.gz GWAS_427.raw.g.vcf.gz GWAS_428.raw.g.vcf.gz GWAS_429.raw.g.vcf.gz GWAS_43.raw.g.vcf.gz GWAS_430.raw.g.vcf.gz GWAS_431.raw.g.vcf.gz GWAS_432.raw.g.vcf.gz GWAS_433.raw.g.vcf.gz GWAS_434.raw.g.vcf.gz GWAS_435.raw.g.vcf.gz GWAS_436.raw.g.vcf.gz GWAS_437.raw.g.vcf.gz GWAS_438.raw.g.vcf.gz GWAS_439.raw.g.vcf.gz GWAS_44.raw.g.vcf.gz GWAS_440.raw.g.vcf.gz GWAS_441.raw.g.vcf.gz GWAS_442.raw.g.vcf.gz GWAS_443.raw.g.vcf.gz GWAS_444.raw.g.vcf.gz GWAS_446.raw.g.vcf.gz GWAS_447.raw.g.vcf.gz GWAS_448.raw.g.vcf.gz GWAS_449.raw.g.vcf.gz GWAS_45.raw.g.vcf.gz GWAS_450.raw.g.vcf.gz GWAS_452.raw.g.vcf.gz GWAS_453.raw.g.vcf.gz GWAS_454.raw.g.vcf.gz GWAS_455.raw.g.vcf.gz GWAS_456.raw.g.vcf.gz GWAS_457.raw.g.vcf.gz GWAS_459.raw.g.vcf.gz GWAS_46.raw.g.vcf.gz GWAS_460.raw.g.vcf.gz GWAS_461.raw.g.vcf.gz GWAS_463.raw.g.vcf.gz GWAS_464.raw.g.vcf.gz GWAS_465.raw.g.vcf.gz GWAS_466.raw.g.vcf.gz GWAS_467.raw.g.vcf.gz GWAS_468.raw.g.vcf.gz GWAS_469.raw.g.vcf.gz GWAS_47.raw.g.vcf.gz GWAS_470.raw.g.vcf.gz GWAS_471.raw.g.vcf.gz GWAS_474.raw.g.vcf.gz GWAS_476.raw.g.vcf.gz GWAS_477.raw.g.vcf.gz GWAS_478.raw.g.vcf.gz GWAS_479.raw.g.vcf.gz GWAS_48.raw.g.vcf.gz GWAS_480.raw.g.vcf.gz GWAS_481.raw.g.vcf.gz GWAS_482.raw.g.vcf.gz GWAS_483.raw.g.vcf.gz GWAS_484.raw.g.vcf.gz GWAS_485.raw.g.vcf.gz GWAS_486.raw.g.vcf.gz GWAS_487.raw.g.vcf.gz GWAS_488.raw.g.vcf.gz GWAS_489.raw.g.vcf.gz GWAS_49.raw.g.vcf.gz GWAS_490.raw.g.vcf.gz GWAS_491.raw.g.vcf.gz GWAS_492.raw.g.vcf.gz GWAS_493.raw.g.vcf.gz GWAS_494.raw.g.vcf.gz GWAS_495.raw.g.vcf.gz GWAS_496.raw.g.vcf.gz GWAS_497.raw.g.vcf.gz GWAS_498.raw.g.vcf.gz GWAS_499.raw.g.vcf.gz GWAS_5.raw.g.vcf.gz GWAS_50.raw.g.vcf.gz GWAS_500.raw.g.vcf.gz GWAS_501.raw.g.vcf.gz GWAS_502.raw.g.vcf.gz GWAS_503.raw.g.vcf.gz GWAS_504.raw.g.vcf.gz GWAS_505.raw.g.vcf.gz GWAS_506.raw.g.vcf.gz GWAS_507.raw.g.vcf.gz GWAS_508.raw.g.vcf.gz GWAS_509.raw.g.vcf.gz GWAS_51.raw.g.vcf.gz GWAS_510.raw.g.vcf.gz GWAS_511.raw.g.vcf.gz GWAS_512.raw.g.vcf.gz GWAS_513.raw.g.vcf.gz GWAS_516.raw.g.vcf.gz GWAS_517.raw.g.vcf.gz GWAS_519.raw.g.vcf.gz GWAS_52.raw.g.vcf.gz GWAS_520.raw.g.vcf.gz GWAS_521.raw.g.vcf.gz GWAS_522.raw.g.vcf.gz GWAS_523.raw.g.vcf.gz GWAS_524.raw.g.vcf.gz GWAS_525.raw.g.vcf.gz GWAS_526.raw.g.vcf.gz GWAS_527.raw.g.vcf.gz GWAS_528.raw.g.vcf.gz GWAS_53.raw.g.vcf.gz GWAS_530.raw.g.vcf.gz GWAS_531.raw.g.vcf.gz GWAS_533.raw.g.vcf.gz GWAS_535.raw.g.vcf.gz GWAS_537.raw.g.vcf.gz GWAS_538.raw.g.vcf.gz GWAS_539.raw.g.vcf.gz GWAS_54.raw.g.vcf.gz GWAS_540.raw.g.vcf.gz GWAS_541.raw.g.vcf.gz GWAS_542.raw.g.vcf.gz GWAS_543.raw.g.vcf.gz GWAS_544.raw.g.vcf.gz GWAS_545.raw.g.vcf.gz GWAS_546.raw.g.vcf.gz GWAS_547.raw.g.vcf.gz GWAS_549.raw.g.vcf.gz GWAS_55.raw.g.vcf.gz GWAS_551.raw.g.vcf.gz GWAS_552.raw.g.vcf.gz GWAS_554.raw.g.vcf.gz GWAS_555.raw.g.vcf.gz GWAS_56.raw.g.vcf.gz GWAS_57.raw.g.vcf.gz GWAS_58.raw.g.vcf.gz GWAS_59.raw.g.vcf.gz GWAS_6.raw.g.vcf.gz GWAS_60.raw.g.vcf.gz GWAS_61.raw.g.vcf.gz GWAS_62.raw.g.vcf.gz GWAS_65.raw.g.vcf.gz GWAS_66.raw.g.vcf.gz GWAS_67.raw.g.vcf.gz GWAS_68.raw.g.vcf.gz GWAS_69.raw.g.vcf.gz GWAS_71.raw.g.vcf.gz GWAS_72.raw.g.vcf.gz GWAS_73.raw.g.vcf.gz GWAS_74.raw.g.vcf.gz GWAS_75.raw.g.vcf.gz GWAS_77.raw.g.vcf.gz GWAS_8.raw.g.vcf.gz GWAS_80.raw.g.vcf.gz GWAS_81.raw.g.vcf.gz GWAS_82.raw.g.vcf.gz GWAS_84.raw.g.vcf.gz GWAS_85.raw.g.vcf.gz GWAS_86.raw.g.vcf.gz GWAS_88.raw.g.vcf.gz GWAS_89.raw.g.vcf.gz GWAS_9.raw.g.vcf.gz GWAS_90.raw.g.vcf.gz GWAS_91.raw.g.vcf.gz GWAS_92.raw.g.vcf.gz GWAS_94.raw.g.vcf.gz GWAS_95.raw.g.vcf.gz GWAS_96.raw.g.vcf.gz GWAS_98.raw.g.vcf.gz GWAS_99.raw.g.vcf.gz">
##SentieonCommandLine.Haplotyper=<ID=Haplotyper,Version="sentieon-genomics-201808.01",Date="2019-03-26T03:47:47Z",CommandLine="/usr/local/sentieon-genomics-201808.01/libexec/driver -r /annoroad/ref//Zea_mays.B73_RefGen_v4.dna.toplevel.fa -t 32 -i /annoroad/out/test//GWAS_1.rmdup.bam -q /annoroad/out/test//GWAS_1.recal_data.table --algo Haplotyper -d /annoroad/ref//zea_mays.resort.vcf --emit_conf=10 --call_conf=20 --emit_mode=gvcf /annoroad/out/test//GWAS_1.raw.g.vcf.gz">
...
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  GWAS_1  GWAS_10 GWAS_100    GWAS_101    GWAS_102    GWAS_105    GWAS_108    GWAS_109    GWAS_11 GWAS_110    GWAS_111
1   1485    .   C   G   47.89   PASS    AC=2;AF=0.003;AN=698;BaseQRankSum=2.362;ClippingRankSum=-0.000;DP=1987;ExcessHet=3.1978;FS=0.000;InbreedingCoeff=-0.0721;MLEAC=2;MLEAF=0.003;MQ=26.14;MQRankSum=0.619;QD=2.52;ReadPosRankSum=2.100;SOR=0.093    GT:AD:DP:GQ:PGT:PID:PL  0/0:2,0:2:6:.:.:0,6,49  0/0:2,0:2:6:.:.:0,6,42  0/0:9,0:9:24:.:.:0,24,360   0/0:8,0:8:24:.:.:0,24,214   0/0:3,0:3:0:.:.:0,0,32  0/0:6,0:6:18:.:.:0,18,132   0/0:4,0:4:12:.:.:0,12,107   0/0:7,0:7:21:.:.:0,21,172   0/0:7,0:7:21:.:.:0,21,168   0/0:10,0:10:30:.:.:0,30,252 0/0:4,0:4:12:.:.:0,12,107
1   1670    .   A   G   128.83  PASS    AC=1;AF=0.002;AN=502;BaseQRankSum=-0.000;ClippingRankSum=-0.000;DP=1164;ExcessHet=3.0472;FS=3.332;InbreedingCoeff=-0.1575;MLEAC=1;MLEAF=0.002;MQ=7.95;MQRankSum=1.834;QD=21.47;ReadPosRankSum=-0.000;SOR=0.061  GT:AD:DP:GQ:PGT:PID:PL  ./.:0,0:0:.:.:.:.   0/0:2,0:2:6:.:.:0,6,57  0/0:15,0:15:0:.:.:0,0,220   0/0:2,0:2:6:.:.:0,6,51  ./.:1,0:1:.:.:.:.   0/0:3,0:3:0:.:.:0,0,23  0/0:5,0:5:0:.:.:0,0,21  0/0:3,0:3:0:.:.:0,0,24  0/0:7,0:7:0:.:.:0,0,115 0/0:8,0:8:24:.:.:0,24,209   0/0:5,0:5:0:.:.:0,0,7
1   1690    .   C   T   1394.17 PASS    AC=30;AF=0.054;AN=552;BaseQRankSum=-0.435;ClippingRankSum=-0.000;DP=2082;ExcessHet=13.8698;FS=5.922;InbreedingCoeff=-0.2287;MLEAC=60;MLEAF=0.109;MQ=25.64;MQRankSum=1.383;QD=8.25;ReadPosRankSum=-0.674;SOR=1.186   GT:AD:DP:GQ:PGT:PID:PL  ./.:0,0:0:.:.:.:.   0/0:2,0:2:6:.:.:0,6,57  0/0:21,0:21:0:.:.:0,0,102   ./.:2,0:2:.:.:.:.   0/0:4,0:4:0:.:.:0,0,69  ./.:10,0:10:.:.:.:. 0/0:11,0:11:0:.:.:0,0,115   0/0:4,0:4:0:.:.:0,0,70  0/0:3,1:4:2:.:.:0,2,107 0/0:9,0:9:15:.:.:0,15,225   0/0:3,0:3:9:.:.:0,9,78
1   1691    .   C   T   465.30  PASS    AC=11;AF=0.019;AN=580;BaseQRankSum=-1.383;ClippingRankSum=-0.000;DP=2172;ExcessHet=0.4527;FS=17.625;InbreedingCoeff=-0.0760;MLEAC=13;MLEAF=0.022;MQ=22.05;MQRankSum=1.036;QD=8.02;ReadPosRankSum=-0.000;SOR=1.453   GT:AD:DP:GQ:PGT:PID:PL  ./.:0,0:0:.:.:.:.   0/0:2,0:2:6:.:.:0,6,57  0/0:22,0:22:42:.:.:0,42,630 ./.:2,0:2:.:.:.:.   0/0:4,0:4:9:.:.:0,9,135 0/0:10,0:10:24:.:.:0,24,360 0/0:11,0:11:7:.:.:0,7,235   0/0:4,0:4:6:.:.:0,6,90  0/0:9,0:9:9:.:.:0,9,135 0/0:9,0:9:15:.:.:0,15,225   0/0:4,0:4:6:.:.:0,6,90
1   1692    .   A   G   312.80  PASS    AC=3;AF=0.005;AN=570;BaseQRankSum=0.431;ClippingRankSum=-0.000;DP=2210;ExcessHet=5.6950;FS=0.000;InbreedingCoeff=-0.1391;MLEAC=5;MLEAF=0.009;MQ=15.42;MQRankSum=0.674;QD=14.90;ReadPosRankSum=-0.674;SOR=0.836  GT:AD:DP:GQ:PGT:PID:PL  ./.:0,0:0:.:.:.:.   0/0:2,0:2:6:.:.:0,6,57  0/0:22,0:22:0:.:.:0,0,171   ./.:2,0:2:.:.:.:.   0/0:4,0:4:9:.:.:0,9,135 0/0:10,0:10:0:.:.:0,0,96    0/0:11,0:11:21:.:.:0,21,247 0/0:4,0:4:6:.:.:0,6,90  0/0:9,0:9:9:.:.:0,9,135 0/0:9,0:9:15:.:.:0,15,225   0/0:4,0:4:6:.:.:0,6,90
1   1713    .   C   T   75.67   PASS    AC=1;AF=0.002;AN=614;BaseQRankSum=-1.068;ClippingRankSum=-0.000;DP=3161;ExcessHet=6.9112;FS=2.363;InbreedingCoeff=-0.1140;MLEAC=1;MLEAF=0.002;MQ=13.36;MQRankSum=-0.967;QD=18.92;ReadPosRankSum=-0.180;SOR=0.223    GT:AD:DP:GQ:PGT:PID:PL  0/0:4,0:4:6:.:.:0,6,90  0/0:4,0:4:0:.:.:0,0,50  0/0:28,0:28:34:.:.:0,34,635 ./.:2,0:2:.:.:.:.   0/0:5,0:5:12:.:.:0,12,180   0/0:11,0:11:27:.:.:0,27,405 0/0:13,0:13:24:.:.:0,24,360 0/0:11,0:11:0:.:.:0,0,145   0/0:16,0:16:0:.:.:0,0,273   0/0:15,0:15:0:.:.:0,0,263   0/0:4,0:4:6:.:.:0,6,90
1   1729    .   C   A   141.26  PASS    AC=2;AF=0.003;AN=634;BaseQRankSum=-0.859;ClippingRankSum=0.000;DP=3881;ExcessHet=17.7727;FS=3.971;InbreedingCoeff=-0.1353;MLEAC=3;MLEAF=0.005;MQ=21.64;MQRankSum=-1.373;QD=3.72;ReadPosRankSum=0.000;SOR=0.636  GT:AD:DP:GQ:PGT:PID:PL  0/0:7,0:7:0:.:.:0,0,26  0/0:4,0:4:9:.:.:0,9,135 0/0:30,0:30:60:.:.:0,60,763 ./.:2,0:2:.:.:.:.   0/0:7,0:7:9:.:.:0,9,135 0/0:13,0:13:30:.:.:0,30,450 0/0:16,0:16:4:.:.:0,4,333   0/0:13,0:13:0:.:.:0,0,259   0/0:20,0:20:0:.:.:0,0,373   0/0:17,0:17:11:.:.:0,11,338 0/0:5,0:5:6:.:.:0,6,90
1   1741    .   C   A   97.45   PASS    AC=2;AF=0.003;AN=710;BaseQRankSum=-0.000;ClippingRankSum=-0.000;DP=4707;ExcessHet=7.6776;FS=0.000;InbreedingCoeff=-0.0878;MLEAC=2;MLEAF=0.003;MQ=18.37;MQRankSum=-1.383;QD=8.12;ReadPosRankSum=-0.674;SOR=0.446 GT:AD:DP:GQ:PGT:PID:PL  0/0:9,0:9:26:.:.:0,26,211   0/0:5,0:5:15:.:.:0,15,121   0/0:36,0:36:29:.:.:0,29,759 0/0:7,0:7:0:.:.:0,0,107 0/0:7,0:7:21:.:.:0,21,164   0/0:15,0:15:44:.:.:0,44,343 0/0:18,0:18:37:.:.:0,37,415 0/0:15,0:15:30:.:.:0,30,321 0/0:23,0:23:0:.:.:0,0,389   0/0:16,0:16:0:.:.:0,0,259   0/0:6,0:6:0:.:.:0,0,106
1   1742    .   C   T   594.16  PASS    AC=22;AF=0.031;AN=704;BaseQRankSum=0.609;ClippingRankSum=0.000;DP=4786;ExcessHet=7.8054;FS=29.642;InbreedingCoeff=-0.0801;MLEAC=23;MLEAF=0.033;MQ=33.83;MQRankSum=0.282;QD=2.42;ReadPosRankSum=0.140;SOR=0.767  GT:AD:DP:GQ:PGT:PID:PL  0/0:10,0:10:12:.:.:0,12,182 0/0:5,0:5:0:.:.:0,0,74  0/1:11,2:13:7:.:.:7,0,356   0/0:7,0:7:9:.:.:0,9,141 0/0:7,0:7:21:.:.:0,21,164   0/0:15,0:15:44:.:.:0,44,343 0/0:18,0:18:40:.:.:0,40,415 0/0:15,0:15:15:.:.:0,15,295 0/0:24,0:24:71:.:.:0,71,575 0/0:21,0:21:63:.:.:0,63,505 0/0:6,0:6:18:.:.:0,18,150
1   1749    .   G   C   473.80  PASS    AC=21;AF=0.029;AN=720;BaseQRankSum=-0.524;ClippingRankSum=0.000;DP=5809;ExcessHet=31.5432;FS=12.799;InbreedingCoeff=-0.1526;MLEAC=33;MLEAF=0.046;MQ=30.30;MQRankSum=0.360;QD=2.48;ReadPosRankSum=0.549;SOR=0.930    GT:AD:DP:GQ:PGT:PID:PL  0/0:11,0:11:0:.:.:0,0,82    0/0:5,0:5:0:.:.:0,0,34  0/0:47,0:47:35:.:.:0,35,991 0/0:9,0:9:0:.:.:0,0,65  0/0:10,0:10:3:.:.:0,3,205   0/0:19,0:19:43:.:.:0,43,440 0/0:22,0:22:0:.:.:0,0,427   0/0:18,0:18:26:.:.:0,26,424 0/1:11,3:14:36:.:.:36,0,357 0/0:25,0:25:0:.:.:0,0,369   0/0:8,0:8:8:.:.:0,8,168
1   1757    .   C   A,T 597.11  PASS    AC=8,9;AF=0.011,0.012;AN=724;BaseQRankSum=-1.044;ClippingRankSum=0.000;DP=7168;ExcessHet=0.6885;FS=8.671;InbreedingCoeff=0.0588;MLEAC=8,10;MLEAF=0.011,0.014;MQ=26.84;MQRankSum=0.598;QD=3.18;ReadPosRankSum=0.468;SOR=1.402    GT:AD:DP:GQ:PGT:PID:PL  0/0:16,0,0:16:23:.:.:0,23,341,23,341,341    0/0:7,0,0:7:3:.:.:0,3,145,3,145,145 0/0:56,0,0:56:99:.:.:0,100,1255,100,1255,1255   0/0:14,0,0:14:0:.:.:0,0,290,0,290,290   0/0:13,0,0:13:23:.:.:0,23,281,23,281,281    0/0:24,0,0:24:55:.:.:0,55,539,55,539,539    0/0:29,0,0:29:57:.:.:0,57,676,57,676,676    0/0:26,0,0:26:48:.:.:0,48,584,48,584,584    0/0:43,0,0:43:0:.:.:0,0,706,0,706,706   0/0:30,0,0:30:0:.:.:0,0,342,0,342,342   0/0:11,0,0:11:18:.:.:0,18,243,18,243,243
1   1758    .   T   C   310.84  PASS    AC=9;AF=0.012;AN=726;BaseQRankSum=-1.068;ClippingRankSum=-0.000;DP=7230;ExcessHet=3.9755;FS=7.329;InbreedingCoeff=-0.0411;MLEAC=9;MLEAF=0.012;MQ=27.08;MQRankSum=0.088;QD=2.43;ReadPosRankSum=1.139;SOR=1.080   GT:AD:DP:GQ:PGT:PID:PL  0/0:17,0:17:33:.:.:0,33,362 0/0:7,0:7:3:.:.:0,3,145 0/0:55,0:55:82:.:.:0,82,1196    0/0:14,0:14:27:.:.:0,27,301 0/0:13,0:13:39:.:.:0,39,318 0/0:24,0:24:53:.:.:0,53,543 0/0:29,0:29:72:.:.:0,72,673 0/0:26,0:26:78:.:.:0,78,678 0/0:43,0:43:57:.:.:0,57,901 0/0:33,0:33:85:.:.:0,85,766 0/0:11,0:11:33:.:.:0,33,284
1   1765    .   A   T,* 244.24  PASS    AC=6,2;AF=0.008,0.003;AN=728;BaseQRankSum=-1.421;ClippingRankSum=-0.000;DP=8464;ExcessHet=3.1996;FS=6.249;InbreedingCoeff=0.0121;MLEAC=6,2;MLEAF=0.008,0.003;MQ=30.99;MQRankSum=0.782;QD=2.68;ReadPosRankSum=1.198;SOR=0.257    GT:AD:DP:GQ:PGT:PID:PL  0/0:22,0,0:22:63:.:.:0,63,945,63,945,945    0/0:8,0,0:8:8:.:.:0,8,178,8,178,178 0/0:61,0,0:61:99:.:.:0,106,1370,106,1370,1370   0/0:16,0,0:16:0:.:.:0,0,218,0,218,218   0/0:14,0,0:14:42:.:.:0,42,322,42,322,322    0/0:25,0,0:25:72:.:.:0,72,1080,72,1080,1080 0/0:36,0,0:36:78:.:.:0,78,826,78,826,826    0/0:31,0,0:31:79:.:.:0,79,740,79,740,740    0/0:54,0,0:54:28:.:.:0,28,970,28,970,970    0/0:35,0,0:35:72:.:.:0,72,755,72,755,755    0/0:11,0,0:11:17:.:.:0,17,244,17,244,244

gvcf

记录变异的原始信息，有无变异都与记录

##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="The phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Combined depth across samples">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts, for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS mapping quality">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##SentieonCommandLine.Haplotyper=<ID=Haplotyper,Version="sentieon-genomics-201808.01",Date="2019-03-26T08:38:59Z",CommandLine="/usr/local/sentieon-genomics-201808.01/libexec/driver -r /annoroad/ref//Zea_mays.B73_RefGen_v4.dna.toplevel.fa -t 32 -i /annoroad/out/test//GWAS_96.rmdup.bam -q /annoroad/out/test//GWAS_96.recal_data.table --algo Haplotyper -d /annoroad/ref//zea_mays.resort.vcf --emit_conf=10 --call_conf=20 --emit_mode=gvcf /annoroad/out/test//GWAS_96.raw.g.vcf.gz">
##contig=<ID=1,length=307041717,assembly=unknown>
##contig=<ID=2,length=244442276,assembly=unknown>
##contig=<ID=3,length=235667834,assembly=unknown>
##contig=<ID=4,length=246994605,assembly=unknown>
##contig=<ID=5,length=223902240,assembly=unknown>
##contig=<ID=6,length=174033170,assembly=unknown>
##contig=<ID=7,length=182381542,assembly=unknown>
##contig=<ID=8,length=181122637,assembly=unknown>
##contig=<ID=9,length=159769782,assembly=unknown>
##contig=<ID=10,length=150982314,assembly=unknown>
##contig=<ID=Pt,length=140384,assembly=unknown>
##contig=<ID=Mt,length=569630,assembly=unknown>
....
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  GWAS_96
1   1   .   T   <NON_REF> .   .   END=1234   GT:DP:GQ:MIN_DP:PL  0/0:0:0:0:0,0,0
1   1235    .   A   <NON_REF> .   .   END=1239   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,27
1   1240    .   T   <NON_REF> .   .   END=1240   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,26
1   1241    .   C   <NON_REF> .   .   END=1241   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,28
1   1242    .   A   <NON_REF> .   .   END=1242   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,25
1   1243    .   T   <NON_REF> .   .   END=1245   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,27
1   1246    .   A   <NON_REF> .   .   END=1246   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,25
1   1247    .   T   <NON_REF> .   .   END=1251   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,27
1   1252    .   A   <NON_REF> .   .   END=1252   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,13
1   1253    .   T   <NON_REF> .   .   END=1257   GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,27
1   1734    .   T   TC,<NON_REF>  8.41    .   BaseQRankSum=0.253;ClippingRankSum=-0.000;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.000;MQRankSum=-0.431;RAW_MQ=5890.00;ReadPosRankSum=-0.842  GT:AD:DP:GQ:PL:SB   0/1:4,2,0:6:45:45,0,110,57,116,173:1,3,1,1

anno

变异信息的注释文件

Chr  Start   End Ref Alt Func.ensGene    Gene.ensGene    GeneDetail.ensGene  ExonicFunc.ensGene  AAChange.ensGene
1   1485    1485    C   G   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42804  .   .
1   1670    1670    A   G   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42619  .   .
1   1690    1690    C   T   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42599  .   .
1   1691    1691    C   T   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42598  .   .
1   1692    1692    A   G   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42597  .   .
1   1713    1713    C   T   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42576  .   .
1   1729    1729    C   A   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42560  .   .
1   1741    1741    C   A   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42548  .   .
1   1742    1742    C   T   intergenic  NONE,Zm00001d027230 dist=NONE;dist=42547  .   .
1       50829   50829   G       A       downstream      Zm00001d027230,Zm00001d027231   .       .       .
1       50846   50846   C       G       downstream      Zm00001d027231  .       .       .
1       51053   51053   A       T       UTR3    Zm00001d027231  Zm00001d027231_T002:c.*103T>A,Zm00001d027231_T001:c.*103T>A,Zm00001d027231_T003:c.*731T>A,Zm00001d027231_T004:c.*68T>A,Zm00001d027231_T005:c.*103T>A,Zm00001d027231_T006:c.*731T>A
1       51407   51407   G       C       exonic  Zm00001d027231  .       nonsynonymous SNV       Zm00001d027231:Zm00001d027231_T001:exon1:c.C76G:p.R26G,Zm00001d027231:Zm00001d027231_T002:exon8:c.C1504G:p.R502G,Zm00001d027231:Zm00001d027231_T004:exon8:c.C1462G:p.R488G,Zm00001d027231:Zm00001d027231_T005:exon8:c.C1462G:p.R488G,Zm00001d027231:Zm00001d027231_T007:exon8:c.C1504G:p.R502G
1       51431   51431   A       T       exonic  Zm00001d027231  .       nonsynonymous SNV       Zm00001d027231:Zm00001d027231_T001:exon1:c.T52A:p.F18I,Zm00001d027231:Zm00001d027231_T002:exon8:c.T1480A:p.F494I,Zm00001d027231:Zm00001d027231_T004:exon8:c.T1438A:p.F480I,Zm00001d027231:Zm00001d027231_T005:exon8:c.T1438A:p.F480I,Zm00001d027231:Zm00001d027231_T007:exon8:c.T1480A:p.F494I
1       51456   51456   C       T       exonic  Zm00001d027231  .       synonymous SNV  Zm00001d027231:Zm00001d027231_T001:exon1:c.G27A:p.L9L
1       51470   51470   G       A       exonic  Zm00001d027231  .       nonsynonymous SNV       Zm00001d027231:Zm00001d027231_T001:exon1:c.C13T:p.R5W
1       51488   51488   A       T       UTR5    Zm00001d027231  Zm00001d027231_T001:c.-6T>A     .       .
1       51505   51505   A       G       UTR5    Zm00001d027231  Zm00001d027231_T001:c.-23T>C    .       .
1       51571   51571   A       C       UTR5    Zm00001d027231  Zm00001d027231_T001:c.-89T>G    .       .
1       51732   51732   T       C       UTR5    Zm00001d027231  Zm00001d027231_T001:c.-250A>G   .       .
1       51750   51750   A       T       UTR5    Zm00001d027231  Zm00001d027231_T001:c.-268T>A   .       .
1       51759   51759   T       C       UTR5    Zm00001d027231  Zm00001d027231_T001:c.-277A>G   .       .
1       51782   51782   C       A       UTR5    Zm00001d027231  Zm00001d027231_T001:c.-300G>T   .       .
1       51784   51784   G       A       UTR5    Zm00001d027231  Zm00001d027231_T001:c.-302C>T   .       .
1       51856   51856   C       G       UTR5;UTR3       Zm00001d027231;Zm00001d027231   Zm00001d027231_T001:c.-374G>C;Zm00001d027231_T008:c.*13G>C      .       .
1       52023   52023   G       A       intronic        Zm00001d027231  .       .       .
1       52046   52046   A       G       intronic        Zm00001d027231  .       .       .
1       52334   52334   T       C       intronic        Zm00001d027231  .       .       .
1       52360   52360   G       A       intronic        Zm00001d027231  .       .       .
1       52463   52463   C       T       exonic  Zm00001d027231  .       synonymous SNV  Zm00001d027231:Zm00001d027231_T002:exon5:c.G1125A:p.R375R,Zm00001d027231:Zm00001d027231_T004:exon5:c.G1083A:p.R361R,Zm00001d027231:Zm00001d027231_T005:exon5:c.G1083A:p.R361R,Zm00001d027231:Zm00001d027231_T007:exon5:c.G1125A:p.R375R,Zm00001d027231:Zm00001d027231_T008:exon5:c.G1083A:p.R361R
1       52472   52472   A       G       exonic  Zm00001d027231  .       synonymous SNV  Zm00001d027231:Zm00001d027231_T002:exon5:c.T1116C:p.I372I,Zm00001d027231:Zm00001d027231_T004:exon5:c.T1074C:p.I358I,Zm00001d027231:Zm00001d027231_T005:exon5:c.T1074C:p.I358I,Zm00001d027231:Zm00001d027231_T007:exon5:c.T1116C:p.I372I,Zm00001d027231:Zm00001d027231_T008:exon5:c.T1074C:p.I358I
1       52478   52478   G       A       exonic  Zm00001d027231  .       synonymous SNV  Zm00001d027231:Zm00001d027231_T002:exon5:c.C1110T:p.V370V,Zm00001d027231:Zm00001d027231_T004:exon5:c.C1068T:p.V356V,Zm00001d027231:Zm00001d027231_T005:exon5:c.C1068T:p.V356V,Zm00001d027231:Zm00001d027231_T007:exon5:c.C1110T:p.V370V,Zm00001d027231:Zm00001d027231_T008:exon5:c.C1068T:p.V356V
1       52515   52515   A       T       exonic  Zm00001d027231  .       nonsynonymous SNV       Zm00001d027231:Zm00001d027231_T002:exon5:c.T1073A:p.M358K,Zm00001d027231:Zm00001d027231_T004:exon5:c.T1031A:p.M344K,Zm00001d027231:Zm00001d027231_T005:exon5:c.T1031A:p.M344K,Zm00001d027231:Zm00001d027231_T007:exon5:c.T1073A:p.M358K,Zm00001d027231:Zm00001d027231_T008:exon5:c.T1031A:p.M344K
1       52519   52519   A       G       exonic  Zm00001d027231  .       nonsynonymous SNV       Zm00001d027231:Zm00001d027231_T002:exon5:c.T1069C:p.C357R,Zm00001d027231:Zm00001d027231_T004:exon5:c.T1027C:p.C343R,Zm00001d027231:Zm00001d027231_T005:exon5:c.T1027C:p.C343R,Zm00001d027231:Zm00001d027231_T007:exon5:c.T1069C:p.C357R,Zm00001d027231:Zm00001d027231_T008:exon5:c.T1027C:p.C343R
1       52553   52553   G       A       exonic  Zm00001d027231  .       synonymous SNV  Zm00001d027231:Zm00001d027231_T002:exon5:c.C1035T:p.G345G,Zm00001d027231:Zm00001d027231_T007:exon5:c.C1035T:p.G345G
1       52576   52576   T       C       exonic  Zm00001d027231  .       nonsynonymous SNV       Zm00001d027231:Zm00001d027231_T002:exon5:c.A1012G:p.I338V,Zm00001d027231:Zm00001d027231_T007:exon5:c.A1012G:p.I338V
1       52578   52578   G       T       exonic  Zm00001d027231  .       nonsynonymous SNV       Zm00001d027231:Zm00001d027231_T002:exon5:c.C1010A:p.S337Y,Zm00001d027231:Zm00001d027231_T007:exon5:c.C1010A:p.S337Y

downstream   1422
exonic  1700
exonic;splicing 7
Func.ensGene    1
intergenic  89505
intronic    3981
ncRNA_exonic    30
splicing    23
upstream    1835
upstream;downstream 88
UTR3    411
UTR5    463
UTR5;UTR3   534.    98292
ExonicFunc.ensGene  1
nonsynonymous   1082
stopgain    58
stoploss    1
synonymous  566

bed文件

geno文件

图谱分型文件

gwas定位结果文件

LD结果文件

PCA结果文件

structure结果文件

tree结果文件

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二代测序（NGS）常用数据格式

fa

fai

gff

fastq

bam

vcf

gvcf

anno

bed文件

geno文件

图谱分型文件

gwas定位结果文件

LD结果文件

PCA结果文件

structure结果文件

tree结果文件

二代测序（NGS）常用数据格式相关推荐

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