BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525177.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 = 4,328,290 number of mapped reads = 3,859,448 (89.17%) number of supplementary alignments = 13,260 (0.31%) number of secondary alignments = 0 number of mapped bases = 221,039,575 bp number of sequenced bases = 220,973,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 257,686 duplication rate = 4.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3347 >>>>>>> ACTG content number of A's = 55,331,784 bp (25.04%) number of C's = 39,824,096 bp (18.02%) number of T's = 72,446,455 bp (32.79%) number of G's = 53,365,583 bp (24.15%) number of N's = 5,184 bp (0%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,131,656 number of insertions = 15,400 mapped reads with insertion percentage = 0.4% number of deletions = 41,763 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.81% >>>>>>> Coverage mean coverageData = 0.0714X std coverageData = 0.6113X There is a 5.82% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 21789632 0.08742057256499272 1.0506606769935016 chr2 243199373 18503243 0.07608260980179418 0.9983965037266064 chr3 198022430 17382640 0.08778116701224199 0.3652400579322232 chr4 191154276 12588213 0.06585368249884194 0.33881767656631095 chr5 180915260 9997763 0.05526213211643949 0.2871203821960543 chr6 171115067 13897976 0.08122005994948417 0.42014343940238946 chr7 159138663 16664974 0.10471983166026724 1.1586776916045685 chr8 146364022 12814200 0.08755020410685353 0.5338046066322204 chr9 141213431 7494297 0.05307070968341531 0.42958551570819303 chr10 135534747 11964781 0.08827832909888414 0.5893306324011095 chr11 135006516 10234810 0.07580974832355498 0.4629876058039267 chr12 133851895 10113045 0.07555399197000535 0.33967173885966495 chr13 115169878 4863990 0.04223317836630859 0.25785877662858653 chr14 107349540 8437718 0.0786004113291962 0.35440840178710004 chr15 102531392 6132515 0.05981109668344306 0.31309236557873493 chr16 90354753 6082104 0.06731360330319314 0.3565121771687725 chr17 81195210 4210850 0.05186081789800162 0.2980152353294532 chr18 78077248 4764156 0.061018492864912455 0.772394117456468 chr19 59128983 4004616 0.06772678637141451 0.7217412648682977 chr20 63025520 4335338 0.06878702468460395 0.32695848950756756 chr21 48129895 2857458 0.059369711901511524 0.32249368656235916 chr22 51304566 1846085 0.03598285969322886 0.2240374382972874 chrMT 16571 282305 17.03608714018466 10.128505730684429 chrX 155270560 9165552 0.05902955460455607 0.35671845602711244 chrY 59373566 611314 0.01029606340303023 0.26533960161678016