BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524420.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 = 2,839,724 number of mapped reads = 2,618,178 (92.2%) number of supplementary alignments = 10,548 (0.37%) number of secondary alignments = 0 number of mapped bases = 152,910,844 bp number of sequenced bases = 152,868,894 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,337 duplication rate = 5.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6501 >>>>>>> ACTG content number of A's = 37,882,198 bp (24.78%) number of C's = 29,729,043 bp (19.45%) number of T's = 45,572,324 bp (29.81%) number of G's = 39,670,564 bp (25.95%) number of N's = 14,765 bp (0.01%) GC percentage = 45.4% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 774,413 number of insertions = 10,049 mapped reads with insertion percentage = 0.38% number of deletions = 25,309 mapped reads with deletion percentage = 0.96% homopolymer indels = 40.85% >>>>>>> Coverage mean coverageData = 0.0494X std coverageData = 0.4604X There is a 4.05% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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% 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 12069307 0.04842237484335094 0.87504256359022 chr2 243199373 12933777 0.05318178595797613 0.6515912762839888 chr3 198022430 9424277 0.04759196723320686 0.26189545027919275 chr4 191154276 9844940 0.051502588411885694 0.4007871409408506 chr5 180915260 9176516 0.05072273063090421 0.2663501337281505 chr6 171115067 8158896 0.047680757416879015 0.2900046570524474 chr7 159138663 8575065 0.05388423427938439 0.6153339094688558 chr8 146364022 7755429 0.05298726349566972 0.35546390469483863 chr9 141213431 6598419 0.04672656809818607 0.33771701912832236 chr10 135534747 7224877 0.053306455797641324 0.5370215866102053 chr11 135006516 7024536 0.05203108863278866 0.38513016366628555 chr12 133851895 6468340 0.0483246053408508 0.2686361500661809 chr13 115169878 4538754 0.03940921080076164 0.23738057482995717 chr14 107349540 4633499 0.04316272803777268 0.2594289008208219 chr15 102531392 4739524 0.046225101479164546 0.2571610297755527 chr16 90354753 4802805 0.05315497901920002 0.31183837323183683 chr17 81195210 4390859 0.05407780828450348 0.30716522676075725 chr18 78077248 3922231 0.05023526187808259 0.633771701075453 chr19 59128983 3530378 0.05970638798235376 0.5902752667443646 chr20 63025520 3567905 0.056610480960728286 0.3033454919786499 chr21 48129895 2231978 0.04637404673332447 0.36122784124349905 chr22 51304566 2392948 0.0466420084325438 0.26471176155811343 chrMT 16571 35467 2.1403053527246394 2.121488906811123 chrX 155270560 8290139 0.0533915701727359 0.31325821236058426 chrY 59373566 579978 0.009768286445857068 0.3400086824291397