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Fei Zhao edited this page Apr 11, 2021 · 2 revisions

Interval Mapping Module Results

The Interval Mapping Module results are located in the directory 06_regionout, the xxx and yyy in the following file names indicate the pool names in the sample.csv file.

06_regionout
├── xxx_yyy_snpindex_input.txt
├── xxx_yyy_qtlseqr_output.txt
├── xxx_yyy_qtlseqr_raw_region.txt
├── xxx_yyy_qtlseqr_filter_region.txt
├── xxx_yyy_qtlseqr_filter_snpinfo.txt
├── xxx_yyy_qtlseqr_filter_indelinfo.txt
├── xxx_yyy_qtlseqr_filter_snp.bed
├── xxx_yyy_qtlseqr_filter_indel.bed
├── xxx_yyy_qtlseqr_SNPcounts_line.pdf
├── xxx_yyy_qtlseqr_SNPcounts_point.pdf
├── xxx_yyy_qtlseqr_SNPindex_line.pdf
├── xxx_yyy_qtlseqr_SNPindex_point.pdf
└── xxx_pool_vs_yyy_pool_candidateregion_1.pdf
  • xxx_yyy_snpindex_input.txt SNP input file for Interval Mapping analysis
  • xxx_yyy_qtlseqr_output.txt QTLseqr SNP result information obtained by Delta SNPindex analysis
  • xxx_yyy_qtlseqr_raw_region.txt QTLseqr Raw interval result information from Delta SNPindex analysis
  • xxx_yyy_qtlseqr_filter_region.txt High confidence trait-related interval information by filtering
  • xxx_yyy_qtlseqr_filter_snpinfo.txt SNP information in the high confidence interval
  • xxx_yyy_qtlseqr_filter_indelinfo.txt INDEL information in the high confidence interval
  • xxx_yyy_qtlseqr_filter_snp.bed SNP bed format file for the high confidence interval, which can be annotated in Triti-Map online analysis platform
  • xxx_yyy_qtlseqr_filter_indel.bed INDEL bed format file in the high confidence interval
  • *.pdf pdf file for visualization of the results, including all chromosome Delta SNPindex, snp counts plots, and Delta SNPindex plots for each high confidence interval

Generally speaking, the results that are most worthy of further analysis are xxx_yyy_qtlseqr_filter_region.txt, xxx_yyy_qtlseqr_filter_snpinfo.txt and xxx_yyy_qtlseqr_filter_indelinfo.txt.

Results Format Description

xx_yyy_snpindex_input.txt

#CHROM  POSm1   POS     REF     ALT     Res_pool_ref    Res_pool_alt    Res_pool_depth  Res_pool_ratio  Sus_pool_ref    Sus_pool_alt    Sus_pool_depth  Sus_pool_ratiosnpindex
chr1A   1144541 1144542 G       A       13      147     160     0.91875 1       144     145     0.993103        -0.0743534

Left to right: chromosome, SNP postion-1, SNP postion, REF , ALT, pool A Ref number, pool A ALT number, SNPindex of pool A, pool B Ref number, pool B ALT number, SNPindex of pool B, Delta SNPindex.

xxx_yyy_qtlseqr_filter_region.txt

CHROM   qtl     start   end     length  nSNPs   avgSNPs_Mb      peakDeltaSNP    posPeakDeltaSNP avgDeltaSNP
chr7A   7       724111912       730119678       6007766 3262    543     0.954374003095134       729506093       0.812296971085005

Left to right: interval chromosome, qtlseqr raw results interval number, interval start position, interval end position, interval length; number of SNPs in the interval, average number of SNPs per 1Mbp; Delta SNPindex peak; Delta SNPindex peak location; average Delta SNPindex. For more information, please refer to QTLseqr.

xxx_yyy_qtlseqr_filter_snpinfo.txt

CHROM   POS     REF     ALT     AD_REF.Sus_pool AD_ALT.Sus_pool DP.Sus_pool     SNPindex.Sus_pool       AD_REF.Res_pool AD_ALT.Res_pool DP.Res_pool     SNPindex.Res_pool      REF_FRQ DeltaSNP        nSNPs   tricubeDeltaSNP minDP   tricubeDP       CI_99   fisher_p
chr7A   724111912       T       G       0       12      12      1       21      0       21      0       0.636363636363636       -1      445     0.505705636608414     12       20      -0.5    2.8183517084228e-09`

Left to right: chromosome, SNP position, REF, ALT, pool A Ref number, pool A ALT number, pool A depth, SNPindex of pool A, pool B Ref number, pool B ALT number, SNPindex of pool B, qtlseqr total reference allele frequence, Delta SNPindex, SNP count, tricube, Delta SNPindex, min depth, tricube depth, 99% confidence interval Delta SNPindex, fisher test p-value

Figure

All chromosome Delta SNPindex plot

X: Chromosome, Y: Delta SNPindex. The blue line indicates the 99% confidence interval calculated by QTLseqR corresponding to the Delta SNPindex value. The gray dots indicate that the corresponding SNP is below this value, and the black dots indicate that the corresponding SNP is above this value.

All chromosome SNP count plot

X: Chromosome, Y: SNP count.

Candidate interval Delta SNPindex plot

The blue line indicates the 99% confidence interval calculated by QTLseqR corresponding to the Delta SNPindex value. The shaded area indicates the trait-related interval.

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