BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238057.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,388,094 number of mapped reads = 2,166,484 (90.72%) number of supplementary alignments = 18,153 (0.76%) number of secondary alignments = 0 number of mapped bases = 145,407,613 bp number of sequenced bases = 145,338,188 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,129 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3257 >>>>>>> ACTG content number of A's = 39,797,465 bp (27.38%) number of C's = 27,688,256 bp (19.05%) number of T's = 45,232,735 bp (31.12%) number of G's = 32,600,498 bp (22.43%) number of N's = 19,234 bp (0.01%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,089,856 number of insertions = 9,831 mapped reads with insertion percentage = 0.45% number of deletions = 39,279 mapped reads with deletion percentage = 1.79% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.047X std coverageData = 0.3911X There is a 3.91% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 12679234 0.05086941789404809 0.666595689757338 chr2 243199373 11933782 0.04906995381110625 0.42817608499548904 chr3 198022430 10822887 0.054654853998105164 0.2712321151525732 chr4 191154276 9048819 0.04733777966860652 0.2666366340190203 chr5 180915260 7612542 0.04207794301044589 0.24021549461466632 chr6 171115067 8081480 0.04722833670748584 0.31157890580980097 chr7 159138663 8482678 0.05330369025407735 0.6037284072567716 chr8 146364022 5977095 0.04083718743394466 0.4399380638976647 chr9 141213431 5968257 0.04226408888825879 0.3411445331407165 chr10 135534747 7727715 0.05701648596429667 0.4405067097376222 chr11 135006516 7482523 0.05542342119250007 0.38610732102162404 chr12 133851895 5608961 0.04190423303308481 0.24183923207296934 chr13 115169878 5336494 0.04633584833701048 0.24948146063623322 chr14 107349540 4539886 0.042290688902812255 0.2646328480745569 chr15 102531392 4619004 0.04504965659687913 0.24868830651515017 chr16 90354753 3572954 0.03954361980271254 0.25642296751717575 chr17 81195210 3577557 0.04406118291953429 0.2833067761410108 chr18 78077248 4686758 0.06002719255678684 0.6603019166553735 chr19 59128983 2708396 0.04580488049320923 0.4765450221413358 chr20 63025520 2847706 0.04518337968492763 0.2532207162815631 chr21 48129895 1984873 0.04123991959674959 0.25752533337938166 chr22 51304566 1695192 0.033041737454713095 0.20919651202204964 chrMT 16571 35582 2.1472451873755354 2.149246740565899 chrX 155270560 8031900 0.05172841522565514 0.2995135422720144 chrY 59373566 345338 0.005816359421632179 0.14241144783209925