BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236099.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,808,501 number of mapped reads = 2,391,386 (85.15%) number of supplementary alignments = 24,244 (0.86%) number of secondary alignments = 0 number of mapped bases = 151,148,025 bp number of sequenced bases = 151,077,911 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,545 duplication rate = 9.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.4645 >>>>>>> ACTG content number of A's = 43,892,726 bp (29.05%) number of C's = 27,273,256 bp (18.05%) number of T's = 48,404,338 bp (32.04%) number of G's = 31,506,298 bp (20.85%) number of N's = 1,293 bp (0%) GC percentage = 38.91% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,166,414 number of insertions = 11,701 mapped reads with insertion percentage = 0.49% number of deletions = 41,944 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.4991X There is a 2.9% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 16061004 0.06443716744039726 0.44966193617306416 chr2 243199373 10582013 0.04351167879038899 0.7431811691726268 chr3 198022430 18966638 0.09578025075240214 0.48034844850898467 chr4 191154276 7654156 0.04004177233262624 0.3736080205135795 chr5 180915260 12821620 0.07087085964998198 0.4105593755094739 chr6 171115067 6991818 0.04086032938291752 0.3342217900491961 chr7 159138663 5879829 0.03694783460635207 0.4062937265599776 chr8 146364022 14256640 0.09740535826488834 1.0912562715274068 chr9 141213431 5643362 0.039963351644646324 0.48711220458279064 chr10 135534747 2506246 0.018491538557267533 0.5268895695658831 chr11 135006516 9133219 0.06765020882399483 0.6117344452529849 chr12 133851895 8292907 0.06195584306072021 0.3991762226213635 chr13 115169878 5171311 0.04490159310579456 0.32700404405203404 chr14 107349540 2568826 0.023929548277524058 0.2480861821957865 chr15 102531392 3150539 0.030727555127701766 0.267632403365533 chr16 90354753 1484792 0.016432915266781815 0.22546917536700814 chr17 81195210 3155646 0.03886492811583343 0.35570477993218824 chr18 78077248 9178729 0.11755958662887299 0.7737168430827882 chr19 59128983 399845 0.006762250586992169 0.3405935162233316 chr20 63025520 2356038 0.03738228577884006 0.2934174186337506 chr21 48129895 452880 0.009409536422217419 0.20947520840902775 chr22 51304566 293263 0.0057161189123011 0.10069086980716811 chrMT 16571 59526 3.5921791080803813 3.6229184585168475 chrX 155270560 3747802 0.024137235030259437 0.2821950898517882 chrY 59373566 339376 0.005715944364871061 0.2224523698661158