BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716699.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 = 1,615,561 number of mapped reads = 1,428,466 (88.42%) number of supplementary alignments = 4,742 (0.29%) number of secondary alignments = 0 number of mapped bases = 81,281,747 bp number of sequenced bases = 81,257,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,881 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0855 >>>>>>> ACTG content number of A's = 20,384,938 bp (25.09%) number of C's = 16,405,492 bp (20.19%) number of T's = 24,964,240 bp (30.72%) number of G's = 19,502,572 bp (24%) number of N's = 562 bp (0%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 419,236 number of insertions = 5,758 mapped reads with insertion percentage = 0.4% number of deletions = 15,204 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.39% >>>>>>> Coverage mean coverageData = 0.0263X std coverageData = 0.2246X There is a 2.39% 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 6861483 0.027528448966231463 0.26857747946998284 chr2 243199373 6211889 0.0255423725948504 0.3423262318648164 chr3 198022430 4653665 0.023500696360508253 0.1698063383510136 chr4 191154276 4793923 0.025078816442484393 0.1827407291525164 chr5 180915260 4685236 0.025897406332666465 0.17284400430805394 chr6 171115067 4331922 0.025315842000050177 0.20179679364089634 chr7 159138663 4744708 0.029814929386455885 0.3050542775367204 chr8 146364022 4164695 0.028454362917138203 0.21568667642541875 chr9 141213431 2662425 0.01885390774196259 0.16862531029546438 chr10 135534747 3529361 0.026040267002527404 0.2738990007265434 chr11 135006516 2885549 0.02137340541400239 0.19260209792599853 chr12 133851895 3954527 0.029544049413719544 0.18556929217915008 chr13 115169878 2373885 0.020612030169902585 0.15385419218451965 chr14 107349540 2481315 0.02311435149139903 0.16745452535442745 chr15 102531392 3186248 0.031075828951975994 0.1950765982468239 chr16 90354753 2982239 0.03300588957395523 0.20645428146265113 chr17 81195210 3679236 0.04531346122511414 0.2400386183896379 chr18 78077248 1506021 0.019288858644198114 0.24045602998239676 chr19 59128983 2340553 0.03958385348856753 0.2817984138663289 chr20 63025520 2936710 0.046595569540719375 0.2469479862169276 chr21 48129895 996593 0.020706319845493117 0.16414816635461627 chr22 51304566 749150 0.01460201417550243 0.1310446019637996 chrMT 16571 5627 0.33956912678776174 0.6814703475093934 chrX 155270560 4327541 0.027870969229453414 0.19059437613393784 chrY 59373566 237246 0.003995818610591791 0.1068768990536242