BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104287.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 17,910,938 number of mapped reads = 17,215,006 (96.11%) number of supplementary alignments = 20,218 (0.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,725,930 number of mapped paired reads (second in pair) = 8,489,076 number of mapped paired reads (both in pair) = 16,954,452 number of mapped paired reads (singletons) = 260,554 number of mapped bases = 1,272,815,231 bp number of sequenced bases = 1,272,495,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,786,581 duplication rate = 33.94% >>>>>>> Insert size mean insert size = 13,431.0829 std insert size = 1,120,177.2747 median insert size = 93 >>>>>>> Mapping quality mean mapping quality = 53.5629 >>>>>>> ACTG content number of A's = 340,300,453 bp (26.74%) number of C's = 299,845,215 bp (23.56%) number of T's = 344,388,695 bp (27.06%) number of G's = 287,289,676 bp (22.58%) number of N's = 671,162 bp (0.05%) GC percentage = 46.14% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 6,980,303 number of insertions = 140,756 mapped reads with insertion percentage = 0.81% number of deletions = 149,602 mapped reads with deletion percentage = 0.86% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.4112X std coverageData = 7.8551X There is a 13.66% of reference with a coverageData >= 1X There is a 6.94% of reference with a coverageData >= 2X There is a 3.14% of reference with a coverageData >= 3X There is a 2.37% of reference with a coverageData >= 4X There is a 1.5% of reference with a coverageData >= 5X There is a 1.25% of reference with a coverageData >= 6X There is a 0.93% of reference with a coverageData >= 7X There is a 0.81% of reference with a coverageData >= 8X There is a 0.66% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.51% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.37% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 111172754 0.4460279920425956 5.070569829076228 chr2 243199373 97711178 0.40177397167878387 2.2706183521305454 chr3 198022430 81430709 0.411219622948774 2.218197145625685 chr4 191154276 72251337 0.37797395126018524 1.828782163280187 chr5 180915260 72037629 0.3981843709590888 2.3837751882530713 chr6 171115067 78568028 0.4591531849150373 2.4934945493739473 chr7 159138663 63402517 0.3984105169967401 2.4574602180422724 chr8 146364022 55606723 0.37992070892941165 3.195466547960008 chr9 141213431 48905505 0.3463233252933285 2.2647645737774655 chr10 135534747 52395597 0.3865842388004015 2.5633053284873806 chr11 135006516 58891085 0.43620920489496967 2.7505112801229687 chr12 133851895 59810714 0.4468424896039014 2.6107477676509783 chr13 115169878 33465467 0.2905748237399366 2.1414307596965623 chr14 107349540 38065502 0.3545939926710445 2.4110769834326637 chr15 102531392 34308304 0.33461268135323863 2.3025150661084814 chr16 90354753 40683391 0.450262876597095 2.9149329906671846 chr17 81195210 45264455 0.5574769127390643 3.6037248057500872 chr18 78077248 26383326 0.3379131139458194 1.9401149676482423 chr19 59128983 45624599 0.7716114278508731 5.046349420344773 chr20 63025520 24559306 0.38967240571755696 2.3954935249602576 chr21 48129895 13068345 0.27152240826621377 2.14256878567856 chr22 51304566 19964645 0.38913973076002634 2.885724216699131 chrMT 16571 51081788 3082.6014121054855 756.6330142503368 chrX 155270560 46582274 0.30000712305024213 1.5538313095853913 chrY 59373566 1580053 0.026612061670676812 0.8194180898606253