BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617699.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 56,069,220 number of mapped reads = 55,174,318 (98.4%) number of supplementary alignments = 700,488 (1.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,788,405 number of mapped paired reads (second in pair) = 27,385,913 number of mapped paired reads (both in pair) = 54,620,548 number of mapped paired reads (singletons) = 553,770 number of mapped bases = 7,494,968,282 bp number of sequenced bases = 7,490,266,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,909,812 duplication rate = 24.4% >>>>>>> Insert size mean insert size = 71,628.6064 std insert size = 2,526,403.2331 median insert size = 275 >>>>>>> Mapping quality mean mapping quality = 53.614 >>>>>>> ACTG content number of A's = 2,190,456,045 bp (29.24%) number of C's = 1,421,061,426 bp (18.97%) number of T's = 2,245,063,647 bp (29.97%) number of G's = 1,633,379,688 bp (21.81%) number of N's = 305,910 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 82,938,944 number of insertions = 1,167,099 mapped reads with insertion percentage = 2.01% number of deletions = 2,530,250 mapped reads with deletion percentage = 4.43% homopolymer indels = 47.38% >>>>>>> Coverage mean coverageData = 2.4211X std coverageData = 25.1383X There is a 46.69% of reference with a coverageData >= 1X There is a 35.37% of reference with a coverageData >= 2X There is a 27.11% of reference with a coverageData >= 3X There is a 21.41% of reference with a coverageData >= 4X There is a 17.01% of reference with a coverageData >= 5X There is a 13.7% of reference with a coverageData >= 6X There is a 11.11% of reference with a coverageData >= 7X There is a 9.08% of reference with a coverageData >= 8X There is a 7.47% of reference with a coverageData >= 9X There is a 6.18% of reference with a coverageData >= 10X There is a 5.14% of reference with a coverageData >= 11X There is a 4.3% of reference with a coverageData >= 12X There is a 3.61% of reference with a coverageData >= 13X There is a 3.04% of reference with a coverageData >= 14X There is a 2.57% of reference with a coverageData >= 15X There is a 2.19% of reference with a coverageData >= 16X There is a 1.86% of reference with a coverageData >= 17X There is a 1.59% of reference with a coverageData >= 18X There is a 1.37% of reference with a coverageData >= 19X There is a 1.18% of reference with a coverageData >= 20X There is a 1.02% of reference with a coverageData >= 21X There is a 0.88% of reference with a coverageData >= 22X There is a 0.77% of reference with a coverageData >= 23X There is a 0.67% of reference with a coverageData >= 24X There is a 0.58% of reference with a coverageData >= 25X There is a 0.51% of reference with a coverageData >= 26X There is a 0.45% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.35% of reference with a coverageData >= 29X There is a 0.31% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 581386740 2.3325387823206265 31.21992430787046 chr2 243199373 524577415 2.156985063444222 31.13177308668772 chr3 198022430 654805868 3.306725748189233 5.353382331003641 chr4 191154276 395550731 2.0692748249063495 24.23021606643757 chr5 180915260 435715414 2.408395035333117 4.8205211486096085 chr6 171115067 450217795 2.631082130248647 17.7554792294985 chr7 159138663 401049633 2.520126947403096 18.75086795744229 chr8 146364022 542236397 3.704710963736703 13.576168633417712 chr9 141213431 312817789 2.2152127229314327 52.08406501670844 chr10 135534747 234554871 1.7305884741128414 54.74747280505994 chr11 135006516 320374846 2.373032469040235 15.717964126830722 chr12 133851895 254854153 1.9040010826891918 7.20460105764538 chr13 115169878 250736657 2.1771027403536887 4.158485948375606 chr14 107349540 327288157 3.0488081923779085 5.739645254404052 chr15 102531392 105430408 1.0282744235053398 3.714816182528985 chr16 90354753 254594082 2.8177165400474284 37.66263253145146 chr17 81195210 166531897 2.051006420206315 29.73184323484514 chr18 78077248 456099479 5.841643893493787 36.78305325440676 chr19 59128983 110835082 1.874462850138992 16.882436661126114 chr20 63025520 219106252 3.476468770110901 8.830560522487083 chr21 48129895 92194937 1.9155441124481987 10.902701944654586 chr22 51304566 34023099 0.6631592790396083 2.2582013795768225 chrMT 16571 835286 50.406493271377705 30.623852022302437 chrX 155270560 351860176 2.2661100468755957 9.597798258096446 chrY 59373566 17291118 0.2912258630381069 23.264959644122484