BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524729.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 = 1,692,665 number of mapped reads = 1,545,448 (91.3%) number of supplementary alignments = 5,709 (0.34%) number of secondary alignments = 0 number of mapped bases = 88,601,354 bp number of sequenced bases = 88,573,656 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,233 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5834 >>>>>>> ACTG content number of A's = 20,579,387 bp (23.23%) number of C's = 17,895,815 bp (20.2%) number of T's = 28,743,391 bp (32.45%) number of G's = 21,344,188 bp (24.1%) number of N's = 10,875 bp (0.01%) GC percentage = 44.3% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 449,996 number of insertions = 5,464 mapped reads with insertion percentage = 0.35% number of deletions = 17,211 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.75% >>>>>>> Coverage mean coverageData = 0.0286X std coverageData = 0.2573X There is a 2.53% of reference with a coverageData >= 1X There is a 0.24% 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 7062594 0.028335311549735315 0.3530435050790651 chr2 243199373 7496897 0.030826136217053487 0.40877795891260776 chr3 198022430 5787245 0.029225199387766326 0.19110206630813822 chr4 191154276 5627337 0.029438718912047773 0.22237794744802464 chr5 180915260 5202949 0.02875903890031167 0.18808386343813271 chr6 171115067 5040557 0.029457119635175083 0.20863750375310877 chr7 159138663 4881594 0.030675097477726076 0.30693005941685164 chr8 146364022 4419043 0.03019213970493377 0.23853045147320437 chr9 141213431 3740419 0.02648770002621068 0.22318079952476474 chr10 135534747 4330020 0.031947674643167334 0.3070238001287328 chr11 135006516 3985765 0.029522760219958567 0.23225128871686546 chr12 133851895 3990545 0.029813137871525838 0.1943419752004812 chr13 115169878 2733558 0.023735008211087972 0.1705732055205741 chr14 107349540 2669554 0.024867866224671294 0.18023480433423375 chr15 102531392 2621532 0.02556809138024772 0.1794414941966074 chr16 90354753 2703189 0.02991750749404406 0.21265410548040287 chr17 81195210 2538788 0.031267706555596075 0.20599592382388607 chr18 78077248 2337232 0.029934866556772084 0.3629367418435716 chr19 59128983 1943534 0.0328693967220779 0.29082285810708547 chr20 63025520 1960780 0.031110889684051794 0.2061947650617871 chr21 48129895 1164548 0.024195938927354818 0.19340285363067788 chr22 51304566 1101590 0.02147157818272939 0.16360015206758988 chrMT 16571 28088 1.6950093536901816 1.5923701927476837 chrX 155270560 4921051 0.03169339377664381 0.21166372107563122 chrY 59373566 312945 0.0052707799292365225 0.14900094412390097