BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618577.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 63,882,138 number of mapped reads = 61,329,129 (96%) number of supplementary alignments = 294,161 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 30,939,269 number of mapped paired reads (second in pair) = 30,389,860 number of mapped paired reads (both in pair) = 60,237,592 number of mapped paired reads (singletons) = 1,091,537 number of mapped bases = 5,872,949,864 bp number of sequenced bases = 5,868,323,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,564,592 duplication rate = 28.6% >>>>>>> Insert size mean insert size = 103,476.3067 std insert size = 3,231,662.9591 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.4295 >>>>>>> ACTG content number of A's = 1,549,383,494 bp (26.4%) number of C's = 1,347,213,812 bp (22.96%) number of T's = 1,557,063,543 bp (26.53%) number of G's = 1,414,375,768 bp (24.1%) number of N's = 286,797 bp (0%) GC percentage = 47.06% >>>>>>> Mismatches and indels general error rate = 0.0138 number of mismatches = 79,156,404 number of insertions = 1,179,295 mapped reads with insertion percentage = 1.89% number of deletions = 3,390,900 mapped reads with deletion percentage = 5.37% homopolymer indels = 52.53% >>>>>>> Coverage mean coverageData = 1.8971X std coverageData = 11.7985X There is a 24.3% of reference with a coverageData >= 1X There is a 17.66% of reference with a coverageData >= 2X There is a 13.86% of reference with a coverageData >= 3X There is a 11.38% of reference with a coverageData >= 4X There is a 9.56% of reference with a coverageData >= 5X There is a 8.2% of reference with a coverageData >= 6X There is a 7.13% of reference with a coverageData >= 7X There is a 6.28% of reference with a coverageData >= 8X There is a 5.57% of reference with a coverageData >= 9X There is a 4.99% of reference with a coverageData >= 10X There is a 4.5% of reference with a coverageData >= 11X There is a 4.08% of reference with a coverageData >= 12X There is a 3.72% of reference with a coverageData >= 13X There is a 3.4% of reference with a coverageData >= 14X There is a 3.13% of reference with a coverageData >= 15X There is a 2.88% of reference with a coverageData >= 16X There is a 2.67% of reference with a coverageData >= 17X There is a 2.48% of reference with a coverageData >= 18X There is a 2.3% of reference with a coverageData >= 19X There is a 2.15% of reference with a coverageData >= 20X There is a 2.01% of reference with a coverageData >= 21X There is a 1.88% of reference with a coverageData >= 22X There is a 1.77% of reference with a coverageData >= 23X There is a 1.66% of reference with a coverageData >= 24X There is a 1.56% of reference with a coverageData >= 25X There is a 1.48% of reference with a coverageData >= 26X There is a 1.4% of reference with a coverageData >= 27X There is a 1.32% of reference with a coverageData >= 28X There is a 1.25% of reference with a coverageData >= 29X There is a 1.19% of reference with a coverageData >= 30X There is a 1.13% of reference with a coverageData >= 31X There is a 1.07% of reference with a coverageData >= 32X There is a 1.02% of reference with a coverageData >= 33X There is a 0.97% of reference with a coverageData >= 34X There is a 0.92% of reference with a coverageData >= 35X There is a 0.88% of reference with a coverageData >= 36X There is a 0.84% of reference with a coverageData >= 37X There is a 0.81% of reference with a coverageData >= 38X There is a 0.77% of reference with a coverageData >= 39X There is a 0.74% of reference with a coverageData >= 40X There is a 0.71% of reference with a coverageData >= 41X There is a 0.68% of reference with a coverageData >= 42X There is a 0.65% of reference with a coverageData >= 43X There is a 0.62% of reference with a coverageData >= 44X There is a 0.6% of reference with a coverageData >= 45X There is a 0.57% of reference with a coverageData >= 46X There is a 0.55% of reference with a coverageData >= 47X There is a 0.53% of reference with a coverageData >= 48X There is a 0.51% of reference with a coverageData >= 49X There is a 0.49% of reference with a coverageData >= 50X There is a 0.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 550567276 2.208890287980466 10.534776069590077 chr2 243199373 476988900 1.9613080992606013 10.213839088517762 chr3 198022430 361919127 1.8276673354629573 29.87522927721116 chr4 191154276 252041831 1.318525728401702 7.235780162735495 chr5 180915260 307598160 1.700233357871525 7.222625111410705 chr6 171115067 296976786 1.7355384958590467 7.321024541586259 chr7 159138663 287379574 1.8058438382129678 7.691682153111113 chr8 146364022 267722061 1.8291521190911246 7.530332609738978 chr9 141213431 262084627 1.855946882276375 9.269331243227397 chr10 135534747 296304817 2.186190800208599 8.72511269208745 chr11 135006516 308776272 2.287121252725313 9.974819638755996 chr12 133851895 253268013 1.892151119713322 8.130671324719858 chr13 115169878 147062638 1.276919282661739 5.99491065758523 chr14 107349540 178151145 1.6595426957581747 7.68370065964615 chr15 102531392 200163752 1.952219199364815 8.70381853065389 chr16 90354753 223913653 2.4781613093447334 18.045249520563218 chr17 81195210 220989658 2.7217080662763236 11.186321424388463 chr18 78077248 143939910 1.8435576776476548 9.034150376841978 chr19 59128983 148514673 2.511706873091323 12.136807131444804 chr20 63025520 188616563 2.9927014168228996 11.221106293254453 chr21 48129895 75494531 1.568557982517934 15.13013040975804 chr22 51304566 132068080 2.5741973920995647 11.799223439798306 chrMT 16571 81150 4.897109408001931 16.728879295150552 chrX 155270560 283264177 1.8243263694031888 7.236258928602991 chrY 59373566 9062490 0.15263509690490884 6.321556361842019