BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716265.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 = 1,638,643 number of mapped reads = 1,202,090 (73.36%) number of supplementary alignments = 1,264 (0.08%) number of secondary alignments = 0 number of mapped bases = 62,935,914 bp number of sequenced bases = 62,919,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,676 duplication rate = 7.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8784 >>>>>>> ACTG content number of A's = 12,408,159 bp (19.72%) number of C's = 10,424,627 bp (16.57%) number of T's = 21,611,967 bp (34.35%) number of G's = 18,473,511 bp (29.36%) number of N's = 1,159 bp (0%) GC percentage = 45.93% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 432,167 number of insertions = 3,681 mapped reads with insertion percentage = 0.3% number of deletions = 9,518 mapped reads with deletion percentage = 0.79% homopolymer indels = 41.65% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.1942X There is a 1.71% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.05% 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 6057443 0.02430261949076548 0.2313991765985239 chr2 243199373 5447310 0.022398536364647618 0.2736950520242209 chr3 198022430 4135328 0.020883129249550166 0.1695642224448819 chr4 191154276 4136613 0.021640180311739404 0.18378902764429408 chr5 180915260 3828400 0.02116128843968165 0.17047857756374374 chr6 171115067 2859662 0.016711924029460246 0.1766465445136104 chr7 159138663 3695541 0.02322214432579467 0.2214822196076723 chr8 146364022 4048045 0.027657377439381927 0.2044383855105316 chr9 141213431 2844246 0.020141469404563933 0.18139392143306476 chr10 135534747 3265174 0.024091047294314865 0.22513948493951247 chr11 135006516 2710255 0.020074994009918752 0.1938388472452311 chr12 133851895 2909331 0.02173544872114063 0.173753207614927 chr13 115169878 1071121 0.00930035716457041 0.11533279014061208 chr14 107349540 1895149 0.017654002057204903 0.1582742255984971 chr15 102531392 1229112 0.011987665202087572 0.12989947359276624 chr16 90354753 1579872 0.017485211873690808 0.1662430011388686 chr17 81195210 2393955 0.02948394369569338 0.21113546111219633 chr18 78077248 1752451 0.022445091814711503 0.20851527204407708 chr19 59128983 1615203 0.02731660377111509 0.2460946714157747 chr20 63025520 1653521 0.026235737523466685 0.20069614376351097 chr21 48129895 831750 0.017281359122017614 0.16856019890268858 chr22 51304566 709434 0.013827892043760783 0.14588822113283528 chrMT 16571 26669 1.60937782873695 1.8134718943099284 chrX 155270560 2040131 0.013139200373850652 0.13919740524836627 chrY 59373566 200198 0.0033718372246666134 0.10576006203463896