BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524877.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 = 2,254,555 number of mapped reads = 2,064,300 (91.56%) number of supplementary alignments = 9,956 (0.44%) number of secondary alignments = 0 number of mapped bases = 119,562,229 bp number of sequenced bases = 119,523,954 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,283 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8665 >>>>>>> ACTG content number of A's = 29,859,860 bp (24.98%) number of C's = 22,729,407 bp (19.02%) number of T's = 37,956,328 bp (31.76%) number of G's = 28,975,904 bp (24.24%) number of N's = 2,455 bp (0%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 599,927 number of insertions = 6,929 mapped reads with insertion percentage = 0.33% number of deletions = 24,008 mapped reads with deletion percentage = 1.15% homopolymer indels = 44% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.3758X There is a 3.41% of reference with a coverageData >= 1X There is a 0.32% 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 13366498 0.053626739008204916 0.7147438987086039 chr2 243199373 9326511 0.03834923949413307 0.4894269125214397 chr3 198022430 7287104 0.03679938681693786 0.2181858284747628 chr4 191154276 7078270 0.037029095807409505 0.2268469475406463 chr5 180915260 5653443 0.031249121826428573 0.19625383378943864 chr6 171115067 6575050 0.038424728548304865 0.26170731190984253 chr7 159138663 9294679 0.058406164943084884 0.6758895186775556 chr8 146364022 6016421 0.04110587368253655 0.34490800324335 chr9 141213431 4187388 0.029652901783825365 0.25899325877237545 chr10 135534747 6585162 0.04858652224436587 0.39142950257605813 chr11 135006516 5770178 0.04273999634210248 0.29473091923394873 chr12 133851895 5611255 0.041921371378417914 0.23215407760955625 chr13 115169878 2793260 0.024253390283178036 0.17382582847193423 chr14 107349540 4657070 0.043382300473760765 0.23700732844414535 chr15 102531392 2576983 0.025133600058799554 0.18027685295124865 chr16 90354753 3302744 0.036553074302577086 0.24001855799907032 chr17 81195210 2143832 0.026403429463388296 0.18908699215305647 chr18 78077248 2688928 0.034439328599286695 0.4984907890729398 chr19 59128983 2192687 0.03708311708997261 0.47829813447736236 chr20 63025520 2649133 0.04203270357785227 0.22949629640589309 chr21 48129895 1474816 0.030642410501830517 0.20652996471213278 chr22 51304566 966190 0.018832436863416797 0.14971502043911764 chrMT 16571 135253 8.162030052501358 5.126484073815169 chrX 155270560 6887493 0.04435800965746501 0.25942590886637096 chrY 59373566 341881 0.005758134857522286 0.168591259526811