BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104289.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 = 30,435,356 number of mapped reads = 29,378,102 (96.53%) number of supplementary alignments = 34,619 (0.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,886,872 number of mapped paired reads (second in pair) = 14,491,230 number of mapped paired reads (both in pair) = 28,944,214 number of mapped paired reads (singletons) = 433,888 number of mapped bases = 2,173,791,068 bp number of sequenced bases = 2,173,242,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,771,210 duplication rate = 39.83% >>>>>>> Insert size mean insert size = 12,024.752 std insert size = 1,091,504.5593 median insert size = 91 >>>>>>> Mapping quality mean mapping quality = 52.8359 >>>>>>> ACTG content number of A's = 553,867,643 bp (25.49%) number of C's = 542,303,808 bp (24.95%) number of T's = 560,745,539 bp (25.8%) number of G's = 515,184,772 bp (23.71%) number of N's = 1,141,215 bp (0.05%) GC percentage = 48.66% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 12,198,165 number of insertions = 215,899 mapped reads with insertion percentage = 0.73% number of deletions = 249,404 mapped reads with deletion percentage = 0.84% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.7022X std coverageData = 31.5864X There is a 16.38% of reference with a coverageData >= 1X There is a 8.5% of reference with a coverageData >= 2X There is a 4.63% of reference with a coverageData >= 3X There is a 3.52% of reference with a coverageData >= 4X There is a 2.49% of reference with a coverageData >= 5X There is a 2.1% of reference with a coverageData >= 6X There is a 1.66% of reference with a coverageData >= 7X There is a 1.46% of reference with a coverageData >= 8X There is a 1.23% of reference with a coverageData >= 9X There is a 1.1% of reference with a coverageData >= 10X There is a 0.96% of reference with a coverageData >= 11X There is a 0.88% of reference with a coverageData >= 12X There is a 0.78% of reference with a coverageData >= 13X There is a 0.73% of reference with a coverageData >= 14X There is a 0.66% of reference with a coverageData >= 15X There is a 0.61% of reference with a coverageData >= 16X There is a 0.56% of reference with a coverageData >= 17X There is a 0.53% of reference with a coverageData >= 18X There is a 0.49% of reference with a coverageData >= 19X There is a 0.46% of reference with a coverageData >= 20X There is a 0.43% of reference with a coverageData >= 21X There is a 0.41% of reference with a coverageData >= 22X There is a 0.39% of reference with a coverageData >= 23X There is a 0.37% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.33% of reference with a coverageData >= 26X There is a 0.32% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 245841236 0.9863214583525551 15.837249748933884 chr2 243199373 146248329 0.6013515873661401 4.766388620330125 chr3 198022430 110250757 0.5567589338238098 3.76000366154598 chr4 191154276 87244524 0.4564089583850063 3.019141361969687 chr5 180915260 97946917 0.5413966571974084 5.391875436346361 chr6 171115067 131508762 0.7685399322550597 4.901495888349664 chr7 159138663 124791015 0.7841652848371612 5.308796621522095 chr8 146364022 78860508 0.5387970822501721 5.180246978909104 chr9 141213431 72725684 0.5150054317425373 4.269006051404663 chr10 135534747 77666866 0.573040255131033 4.237037940197145 chr11 135006516 101430169 0.7512983225194849 5.833705786924201 chr12 133851895 84418188 0.6306835476628851 4.3013427050456245 chr13 115169878 34957886 0.30353323809199484 5.833592379407856 chr14 107349540 42088402 0.39206876899519083 3.0919196919949004 chr15 102531392 57011702 0.5560414316817234 3.98050751926643 chr16 90354753 73964702 0.8186033334627123 5.399473768328973 chr17 81195210 78575915 0.9677407694370148 6.3033681264474675 chr18 78077248 32080949 0.4108872920316044 3.2708956564037273 chr19 59128983 103247855 1.7461463018905636 9.76339275913388 chr20 63025520 44982046 0.7137116203087257 4.510242225361103 chr21 48129895 25132139 0.5221731524658427 4.679799607650825 chr22 51304566 53829896 1.0492223245782841 9.200081211702743 chrMT 16571 216279085 13051.661637800978 2884.969182531238 chrX 155270560 50519779 0.325366115765925 2.421884412742398 chrY 59373566 2187757 0.036847323605255576 1.5320880816074238