BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716209.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 = 1,633,724 number of mapped reads = 1,445,237 (88.46%) number of supplementary alignments = 5,413 (0.33%) number of secondary alignments = 0 number of mapped bases = 81,809,245 bp number of sequenced bases = 81,783,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,627 duplication rate = 1.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0199 >>>>>>> ACTG content number of A's = 19,912,189 bp (24.35%) number of C's = 17,078,206 bp (20.88%) number of T's = 25,892,828 bp (31.66%) number of G's = 18,900,164 bp (23.11%) number of N's = 586 bp (0%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 429,376 number of insertions = 6,401 mapped reads with insertion percentage = 0.44% number of deletions = 16,072 mapped reads with deletion percentage = 1.1% homopolymer indels = 40.44% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.231X There is a 2.4% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6915051 0.027743365181023962 0.2887466678792001 chr2 243199373 6327668 0.02601843878931382 0.3416776179122799 chr3 198022430 4714625 0.02380854027495774 0.17128721433527688 chr4 191154276 4987821 0.026093169895922183 0.1833540343017574 chr5 180915260 4637081 0.025631231992259803 0.1724031742676633 chr6 171115067 4416241 0.025808603984592428 0.20478718653095573 chr7 159138663 4683576 0.029430786407951662 0.31540502432918555 chr8 146364022 4241144 0.028976683901184404 0.22671321136250164 chr9 141213431 2693787 0.019075997098321334 0.16798251444991913 chr10 135534747 3609084 0.026628477788061242 0.27621512868657855 chr11 135006516 2840715 0.021041317739063793 0.1901066130365631 chr12 133851895 4127525 0.030836507768530284 0.1918365096348749 chr13 115169878 2794815 0.024266892077457962 0.16848179924834955 chr14 107349540 2715286 0.025293876433937212 0.17788549563205994 chr15 102531392 2501466 0.02439707441014748 0.17148980035181943 chr16 90354753 2834636 0.0313722953788607 0.20077329804190697 chr17 81195210 3618473 0.04456510427154508 0.23894687097028797 chr18 78077248 1507940 0.019313436867037116 0.2573256791958749 chr19 59128983 2160927 0.036545986255166946 0.28490548577140773 chr20 63025520 2599652 0.041247608905091146 0.22881282430203148 chr21 48129895 1013935 0.021066636442901028 0.16737313112060045 chr22 51304566 759782 0.014809247192540329 0.1326090110895549 chrMT 16571 192425 11.612153762597309 8.242619601059978 chrX 155270560 4679306 0.030136466307585933 0.19865782696040374 chrY 59373566 236284 0.003979616114012758 0.10485258815906982