BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961016.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 302,308,146 number of mapped reads = 295,295,673 (97.68%) number of supplementary alignments = 680,123 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 147,821,730 number of mapped paired reads (second in pair) = 147,473,943 number of mapped paired reads (both in pair) = 294,316,972 number of mapped paired reads (singletons) = 978,701 number of mapped bases = 29,002,927,097 bp number of sequenced bases = 28,993,927,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,480,819 duplication rate = 8.29% >>>>>>> Insert size mean insert size = 22,081.3471 std insert size = 1,388,908.8704 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.6583 >>>>>>> ACTG content number of A's = 8,540,794,656 bp (29.46%) number of C's = 5,933,261,498 bp (20.46%) number of T's = 8,518,903,200 bp (29.38%) number of G's = 5,983,173,595 bp (20.64%) number of N's = 17,794,603 bp (0.06%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 143,432,027 number of insertions = 2,997,214 mapped reads with insertion percentage = 0.98% number of deletions = 3,550,826 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 9.3688X std coverageData = 102.94X There is a 91.42% of reference with a coverageData >= 1X There is a 90.81% of reference with a coverageData >= 2X There is a 89.46% of reference with a coverageData >= 3X There is a 87.02% of reference with a coverageData >= 4X There is a 83.1% of reference with a coverageData >= 5X There is a 77.57% of reference with a coverageData >= 6X There is a 70.52% of reference with a coverageData >= 7X There is a 62.29% of reference with a coverageData >= 8X There is a 53.4% of reference with a coverageData >= 9X There is a 44.42% of reference with a coverageData >= 10X There is a 35.86% of reference with a coverageData >= 11X There is a 28.13% of reference with a coverageData >= 12X There is a 21.47% of reference with a coverageData >= 13X There is a 15.97% of reference with a coverageData >= 14X There is a 11.61% of reference with a coverageData >= 15X There is a 8.27% of reference with a coverageData >= 16X There is a 5.8% of reference with a coverageData >= 17X There is a 4.01% of reference with a coverageData >= 18X There is a 2.76% of reference with a coverageData >= 19X There is a 1.91% of reference with a coverageData >= 20X There is a 1.33% of reference with a coverageData >= 21X There is a 0.95% of reference with a coverageData >= 22X There is a 0.71% of reference with a coverageData >= 23X There is a 0.54% of reference with a coverageData >= 24X There is a 0.44% of reference with a coverageData >= 25X There is a 0.37% of reference with a coverageData >= 26X There is a 0.32% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2360008968 9.468417605266469 244.4476288914756 chr2 243199373 2483869771 10.213306639569337 64.29610156466504 chr3 198022430 1908151485 9.636037114583434 20.8500474855949 chr4 191154276 1951899110 10.211119263688351 90.49257492855689 chr5 180915260 1738664547 9.610380832440558 9.940905764829248 chr6 171115067 1657599935 9.687048394166249 29.867986241860784 chr7 159138663 1548484299 9.73040912754181 63.041851015353615 chr8 146364022 1455462559 9.944127929198338 100.67360416675426 chr9 141213431 1209931895 8.56810776731287 88.12295825040319 chr10 135534747 1518862255 11.206441806395226 243.1100379602103 chr11 135006516 1305492538 9.669848364948548 40.80844183282941 chr12 133851895 1277503997 9.544160708370995 7.9122422336066744 chr13 115169878 919983150 7.988053525592864 5.7932247943940745 chr14 107349540 854818515 7.962945299998491 9.136890456161733 chr15 102531392 804554859 7.846912475351939 5.967707788095271 chr16 90354753 931755592 10.312192342554464 99.38728323005573 chr17 81195210 777412308 9.574608009511891 38.501241852490345 chr18 78077248 788338201 10.096900456839872 105.17351314798253 chr19 59128983 566612504 9.582652622318905 118.43355293055414 chr20 63025520 598311035 9.493155074325449 33.901858561487124 chr21 48129895 398495339 8.2795804769572 45.29261675763764 chr22 51304566 340541847 6.6376518417483545 7.91436839362469 chrMT 16571 22385712 1350.8968680224489 185.5002658853613 chrX 155270560 1486161815 9.57143334190332 31.218394566557297 chrY 59373566 97624861 1.6442478964460379 95.57315995355452