BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716774.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 = 1,294,848 number of mapped reads = 1,193,521 (92.17%) number of supplementary alignments = 28,914 (2.23%) number of secondary alignments = 0 number of mapped bases = 90,277,586 bp number of sequenced bases = 90,241,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,622 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7526 >>>>>>> ACTG content number of A's = 23,284,491 bp (25.8%) number of C's = 17,900,407 bp (19.84%) number of T's = 26,649,783 bp (29.53%) number of G's = 22,403,549 bp (24.83%) number of N's = 2,992 bp (0%) GC percentage = 44.66% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 607,903 number of insertions = 8,121 mapped reads with insertion percentage = 0.67% number of deletions = 17,778 mapped reads with deletion percentage = 1.46% homopolymer indels = 39.25% >>>>>>> Coverage mean coverageData = 0.0292X std coverageData = 0.2605X There is a 2.55% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9828211 0.03943103917081113 0.46383191501386156 chr2 243199373 8471058 0.03483174276111312 0.2792202270369182 chr3 198022430 5851517 0.02954976868024496 0.1929943495706397 chr4 191154276 4382856 0.02292837017153621 0.22665516308163858 chr5 180915260 4651186 0.02570919667030852 0.17905135420331575 chr6 171115067 5047349 0.02949681222402233 0.2027922597582625 chr7 159138663 5700761 0.03582260207879213 0.3504600751218217 chr8 146364022 5583104 0.03814533055124708 0.2829325220485275 chr9 141213431 2720926 0.019268181367252526 0.18706969885663033 chr10 135534747 4808498 0.035477972301818664 0.3489879572535416 chr11 135006516 3827622 0.02835138712860348 0.23257865390438934 chr12 133851895 3524188 0.026329010881766 0.18087368706467163 chr13 115169878 1703481 0.014791028952900341 0.13333516990188163 chr14 107349540 1781216 0.01659267473339895 0.15106098352497285 chr15 102531392 1854411 0.018086275469662988 0.14874612969721163 chr16 90354753 2755394 0.03049528562155441 0.20395798696389436 chr17 81195210 2248478 0.027692249333427427 0.199101042314408 chr18 78077248 2455099 0.03144448687535708 0.27671967174818923 chr19 59128983 2230890 0.03772921310011369 0.3253053871721867 chr20 63025520 2039676 0.03236270006181623 0.20627836694483065 chr21 48129895 1383331 0.02874161682671446 0.2237211242830881 chr22 51304566 1382624 0.026949336244263326 0.18608362125962408 chrMT 16571 83704 5.051234083640094 3.998784867762068 chrX 155270560 5660293 0.036454386459351985 0.22040755699635756 chrY 59373566 301713 0.005081604834043487 0.17716108997364535