BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716473.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,227,931 number of mapped reads = 2,987,650 (92.56%) number of supplementary alignments = 18,290 (0.57%) number of secondary alignments = 0 number of mapped bases = 174,272,729 bp number of sequenced bases = 174,225,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,576 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6588 >>>>>>> ACTG content number of A's = 43,573,439 bp (25.01%) number of C's = 36,305,605 bp (20.84%) number of T's = 52,063,890 bp (29.88%) number of G's = 42,281,065 bp (24.27%) number of N's = 1,277 bp (0%) GC percentage = 45.11% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 868,992 number of insertions = 11,802 mapped reads with insertion percentage = 0.39% number of deletions = 30,470 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.0563X std coverageData = 0.44X There is a 4.69% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 20627251 0.08275706964036009 0.7173947184690681 chr2 243199373 17800556 0.07319326435927942 0.6183923604004136 chr3 198022430 10852716 0.05480548844896005 0.27280502066819357 chr4 191154276 7254261 0.03794977100067592 0.2590736728581681 chr5 180915260 12618931 0.06975050639730446 0.3083304430440549 chr6 171115067 6494949 0.037956616643232244 0.2585519979396597 chr7 159138663 11832922 0.07435604759353796 0.7874021250036415 chr8 146364022 7647717 0.05225134493776073 0.3690223041372201 chr9 141213431 4802614 0.034009612017712396 0.32889309582541165 chr10 135534747 7860412 0.05799554855110328 0.37212969118122735 chr11 135006516 7470194 0.05533209967435942 0.41983724384560944 chr12 133851895 6860003 0.05125069764608114 0.2681346665392356 chr13 115169878 5124065 0.044491364313158345 0.2462916730450947 chr14 107349540 3713111 0.03458897914234192 0.23587685423473737 chr15 102531392 7539274 0.07353137271363681 0.32407135637612183 chr16 90354753 5172157 0.05724277725600113 0.3005671314339483 chr17 81195210 7508975 0.0924805170157205 0.40805826872992634 chr18 78077248 5572867 0.07137632463685195 0.7584105686008624 chr19 59128983 2725839 0.04609987964785391 0.5714095551060937 chr20 63025520 4535147 0.07195731189524497 0.31751536845495004 chr21 48129895 1570107 0.03262228184790347 0.22791898563039684 chr22 51304566 2019006 0.039353339427917584 0.2293637817543609 chrMT 16571 57626 3.4775209703699232 2.658368381395944 chrX 155270560 6256828 0.04029629312858793 0.28021587372272827 chrY 59373566 355201 0.00598247711784736 0.13648983625157554