+------------------------------------------------------------------------------+ | Result instruction on Genome re-sequencing | +------------------------------------------------------------------------------+ ├── 00.Data ├── genes.gff #Gene structure file ├── Integrated_Function.annotation.xls #Gene annotation file └── sequences.fa #Reference genome file ├── 01.Dataassess │   ├── 01.GC │   │   ├── *.acgtn.pdf #Sample base content distribution map (pdf format) │   │   └── *.acgtn.png #Sample base content distribution map (png format) │   ├── 02.Quality │   │   ├── *.quality.pdf #Sample base quality distribution map (pdf format) │   │   └── *.quality.png #Sample base quality distribution map (png format) │   └── QC_stat.xls #Statistical table of sequencing data for each sample ├── 02.Mapping │   ├── 01.picture │   │   ├── 01.depth_coverage │   │   │   ├── *.sort.depth.cov.txt.png #Distribution map of sequencing reads on chromosome (png format) │   │   │   └── *.sort.depth.cov.txt.png.pdf #Distribution map of sequencing reads on chromosome (pdf format) │   │   ├── 02.insert │   │   │   ├── *.sort.insert.cut.png #Insert size distribution map (png format) │   │   │   └── *.sort.insert.cut.png.pdf #Insert size distribution map (pdf format) │   │   └── 03.depth_distance │   │      ├── *.sort.depth.dis.cut.pdf #Distribution map of sequencing depth and cumulative depth of each sample (pdf format) │   │   └── *.sort.depth.dis.cut.png #Distribution map of sequencing depth and cumulative depth of each sample (png format) │   └── 02.stat │   └── *.map_depth_stat.xls #Statistics of alignment efficiency, coverage depth and coverage ratio of each sample ├── 03.SNP │   ├── 01.SNP_vcf │   │   ├── *.raw.filter.snp.snp.stat #Statistics of each type of SNP in each sample │   │   └── *.raw.filter.snp.vcf #The vcf file is based on hard filtering. (All subsequent analyzes are based on this file) │   ├── 02.anno_list │   │   ├── *.filtered.snp.anno.description.list #Annotation of the SNPs of each sample in different regions of the genome and other related information │   │   ├── *.filtered.snp.Exonic.anno.description.list #Annotation of the SNP in the exon region of each sample and other related information │   │   ├── *.raw.filter.snp.anno.gatk.vcf #SNP annotation vcf files of all samples after filtering (only the annotated SNP variation sites are kept) │   │   └── SNP.anno_stat.xls #Statistics of SNP annotation results │   ├── 03.picture │   │   ├── SNP.anno.All.pie.pdf #Statistics of SNP annotation results pie chart (pdf format) │   │   ├── SNP.anno.All.pie.png #Statistics of SNP annotation results pie chart (png format) │   │   ├── SNP.mutation.distribution.pdf #The plot of SNP conversion and transversion for each sample (pdf format) │   │   ├── SNP.mutation.distribution.png #The plot of SNP conversion and transversion for each sample (png format) │   │   ├── SNP.quality.distribution.png #SNP quality distribution plot (depth and distance cumulative plot, png format) │   │   ├── SNP.quality.distribution.pdf #SNP quality distribution plot (depth and distance cumulative plot, pdf format) │   │   ├── SNP.venn.pdf #Statistical Venn diagram of SNP between samples (pdf format). It will only be displayed within 5 samples │   │   └── SNP.venn.png #Statistical Venn diagram of SNP between samples (png format). It will only be displayed within 5 samples │   └── 04.DEG │   ├── DEG_snp.stat #Statistics of the number of differential SNPs │   ├── *.raw.filter.snp.DEG.snp #SNPs that differ among samples │   └── *.raw.filter.snp.DEG.vcf #SNPs that differ among samples (vcf format) ├── 04.INDEL │   ├── 01.INDEL_vcf │   │   └── *.raw.filter.indel.stat #Statistics of each type of INDEL in each sample │   │   └── *.raw.filter.indel.vcf #The vcf file is based on hard filtering. (Part of the subsequent INDEL annotations are based on this file) │   ├── 02.anno_list │   │   ├── Indel.anno_stat.xls #Statistics of INDEL annotation results │   │   ├── *.filtered.indel.anno.description.list #Annotation of the INDEL of each sample in different regions of the genome and other related information │   │   ├── *.filtered.indel.Exonic.anno.description.list #Annotation of the INDEL in the exon region of each sample and other related information │   │   └── *.raw.filter.indel.anno.gatk.vcf #SNP annotation vcf files of all samples (only the annotated SNP variation sites are kept) │   ├── 03.picture │   │   ├── all.sample.indel.length.distribution.pdf #INDEL length distribution plot for all samples (pdf format) │   │   ├── all.sample.indel.length.distribution.png #INDEL length distribution plot for all samples (png format) │   │   ├── Indel.anno.All.pie.pdf #Statistics of INDEL annotation results pie chart (pdf format) │   │   ├── Indel.anno.All.pie.png #Statistics of INDEL annotation results pie chart (png format) │   │   ├── INDEL.venn.pdf #Statistical Venn diagram of INDEL between samples (pdf format). It will only be displayed within 5 samples │   │   ├── INDEL.venn.png #Statistical Venn diagram of INDEL between samples (png format). It will only be displayed within 5 samples │   │   ├── *.combine.Indel.dis.pdf #Statistical distribution diagram of INDEL length (total, pdf format) │   │   └── *.combine.Indel.dis.png #Statistical distribution diagram of INDEL length (total, png format) │   └── 04.DEG │   ├── DEG_indel.stat #Statistics of the number of differential INDEL │   ├── *.combine.Indel.stat #Distribution statistics of INDEL in coding and non-coding regions │   ├── *.raw.filter.indel.DEG.list #INDELs that differ among samples (list format) │   └── *.raw.filter.indel.DEG.vcf #INDELs that differ among samples (vcf format) ├── 05.Circos │   └── *.circos.png #Distribution of various types of mutations on chromosomes (png format) │   └── *.circos.pdf #Distribution of various types of mutations on chromosomes (pdf format) ├── 06.Diff_analysis │   ├── 01.Non-synonymous_snp_gene │   │   └── *.raw.filter.snp.anno.gatk.*.list #Non-synonymously mutated genes │   ├── 02.CDS_indel_genelist │   │   └── *.raw.filter.indel.anno.gatk.*.list #Genes with non-synonymous or frameshift mutations │   ├── 03.gene.list │   │   └── *.vs.ref.gene.list #Genes for functional annotation │   ├── 04.enrichment │   │   ├── *_enrichment │   │   │   ├── Cog_Anno │   │   │   │   ├── *.Cog.classfy.png #COG classification result plot (png format) │   │   │   │   └── *.Cog.classfy.stat #The statistics of the classification results of genes in the COG database │   │   │   ├── go_enrichment │   │   │   │   ├── *.GO.Biological.stat #Secondary function-biological process enrichment statistical analysis results │   │   │   │   ├── *.GO.Biological.xls #Secondary function-statistics of genes enriched by biological processes │   │   │   │   ├── *.GO.Cellular.stat #Secondary function - cell component enrichment statistical analysis results │   │   │   │   ├── *.GO.Cellular.xls #Secondary function-statistics of enriched genes in cellular components │   │   │   │   ├── *.GO_enrichment.stat.xls #Secondary Functions - Annotation and Statistics of Enriched Genes │   │   │   │   ├── *.GO.list #GO secondary node annotation statistics │   │   │   │   ├── *.GO.list.txt #Gene and GO number correspondence table │   │   │   │   ├── *.GO.Molecular.stat #Secondary function - statistical analysis results of molecular function enrichment │   │   │   │   ├── *.GO.Molecular.xls #Secondary Functions - statistics of enriched genes in molecular functional │   │   │   │   └── *.GO.png #Gene GO classification statistical results chart │   │   │   ├── Graph │   │   │   │   ├── *.topGO_BP.pdf #TopGO Directed acyclic Map of Genes (Biological process level, pdf format) │   │   │   │   ├── *.topGO_BP.png #TopGO Directed acyclic Map of Genes (Biological process level, png format) │   │   │   │   ├── *.topGO_BP.xls #Enrichment Results of topGO directed Acyclic Map of Genes (Biological process level) │   │   │   │   ├── *.topGO_CC.pdf #topGO Directed acyclic map of Genes (Cellular component level, pdf format) │   │   │   │   ├── *.topGO_CC.png #topGO directed acyclic map of genes (Cellular component level, png format) │   │   │   │   ├── *.topGO_CC.xls #topGO acyclic Enrichment of genes (Cellular component level) │   │   │   │   ├── *.topGO_MF.pdf #topGO Directed acyclic Map of Genes (Molecular Function level, pdf format) │   │   │   │   ├── *.topGO_MF.png #topGO directed acyclic Map of Genes (Molecular Function level, png format) │   │   │   │   ├── *.topGO_MF.xls #Enrichment Results of topGO directed acyclic Map of Genes (Molecular Function level) │   │   │   │   └── topGO.map #Gene and GO number correspondence table │   │   │   ├── Kog_Anno │   │   │   │   ├── *.Kog.classfy.png #Kog classification Statistics Result Chart (png format) │   │   │   │   └── *.Kog.classfy.stat #Statistical results of gene classification in Kog database │   │   │   ├── pathway │   │   │   │   ├── kegg_enrichment │   │   │   │   │   ├── *.Kegg.ko #ko results of KEGG enrichment analysis │   │   │   │   │   ├── *.KEGG.stat #Statistical results of KEGG enrichment analysis │   │   │   │   │   └── *.KEGG.xls #Gene statistics of KEGG enrichment analysis │   │   │   │   └── kegg_map │   │   │   │   ├── *.html │   │   │   │   └── *.png │   │   │   └── *.annotation.xls #Annotated results for each sample │   └── Diff_gene.stat #The number of variant gene annotations of different types ├── 07.SV │   ├── all_annotated.sum #SV annotation information file │   ├── *.sv.anno.stat #Statistics files for SV annotations │   ├── *.sv.stat.xls #Statistics files of type SV │   ├── *.bed #SV details for each sample (bed format) │   ├── *.vcf #SV details for each sample (vcf format) │   └── Total.VCF #Integrated results of SV results of all samples (vcf format) ├── 08.CNV │   ├── *.sort.bam.CNV.gene.anno.xls #CNV annotation information file │   └── *.sort.bam_CNVs #CNV result file └── Other #################################Remark 1. For the description of important files, please refer to the relevant Readme files under each directory of the delivery data. 2. To view text files, linux or unix users can use commands such as more and less to view them, and Windows users can use a text editor or WordPad to open and edit text files, such as gedit or editplus. 3. If there is no content in the contract (such as SV or CNV) in the contract, you can ignore it. 4. The Other folder is used to issue the temporary files used in the final report, you can ignore it.