BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695943.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 418,477,858 number of mapped reads = 414,116,976 (98.96%) number of supplementary alignments = 5,425,976 (1.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 208,171,523 number of mapped paired reads (second in pair) = 205,945,453 number of mapped paired reads (both in pair) = 411,015,684 number of mapped paired reads (singletons) = 3,101,292 number of mapped bases = 40,960,395,056 bp number of sequenced bases = 40,949,427,715 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,726,043 duplication rate = 18.3% >>>>>>> Insert size mean insert size = 73,238.1313 std insert size = 2,663,826.0841 median insert size = 314 >>>>>>> Mapping quality mean mapping quality = 54.02 >>>>>>> ACTG content number of A's = 11,545,502,915 bp (28.19%) number of C's = 8,838,644,225 bp (21.58%) number of T's = 11,464,777,017 bp (28%) number of G's = 9,097,840,046 bp (22.22%) number of N's = 2,663,512 bp (0.01%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 212,457,095 number of insertions = 5,281,676 mapped reads with insertion percentage = 1.24% number of deletions = 4,530,411 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 13.2314X std coverageData = 31.8117X There is a 82.14% of reference with a coverageData >= 1X There is a 74.75% of reference with a coverageData >= 2X There is a 68.33% of reference with a coverageData >= 3X There is a 62.64% of reference with a coverageData >= 4X There is a 57.55% of reference with a coverageData >= 5X There is a 52.99% of reference with a coverageData >= 6X There is a 48.89% of reference with a coverageData >= 7X There is a 45.19% of reference with a coverageData >= 8X There is a 41.85% of reference with a coverageData >= 9X There is a 38.83% of reference with a coverageData >= 10X There is a 36.09% of reference with a coverageData >= 11X There is a 33.59% of reference with a coverageData >= 12X There is a 31.33% of reference with a coverageData >= 13X There is a 29.25% of reference with a coverageData >= 14X There is a 27.36% of reference with a coverageData >= 15X There is a 25.63% of reference with a coverageData >= 16X There is a 24.04% of reference with a coverageData >= 17X There is a 22.58% of reference with a coverageData >= 18X There is a 21.23% of reference with a coverageData >= 19X There is a 19.98% of reference with a coverageData >= 20X There is a 18.83% of reference with a coverageData >= 21X There is a 17.77% of reference with a coverageData >= 22X There is a 16.78% of reference with a coverageData >= 23X There is a 15.87% of reference with a coverageData >= 24X There is a 15.02% of reference with a coverageData >= 25X There is a 14.23% of reference with a coverageData >= 26X There is a 13.49% of reference with a coverageData >= 27X There is a 12.8% of reference with a coverageData >= 28X There is a 12.16% of reference with a coverageData >= 29X There is a 11.56% of reference with a coverageData >= 30X There is a 11% of reference with a coverageData >= 31X There is a 10.47% of reference with a coverageData >= 32X There is a 9.98% of reference with a coverageData >= 33X There is a 9.51% of reference with a coverageData >= 34X There is a 9.08% of reference with a coverageData >= 35X There is a 8.67% of reference with a coverageData >= 36X There is a 8.28% of reference with a coverageData >= 37X There is a 7.91% of reference with a coverageData >= 38X There is a 7.57% of reference with a coverageData >= 39X There is a 7.25% of reference with a coverageData >= 40X There is a 6.94% of reference with a coverageData >= 41X There is a 6.65% of reference with a coverageData >= 42X There is a 6.38% of reference with a coverageData >= 43X There is a 6.12% of reference with a coverageData >= 44X There is a 5.87% of reference with a coverageData >= 45X There is a 5.64% of reference with a coverageData >= 46X There is a 5.41% of reference with a coverageData >= 47X There is a 5.2% of reference with a coverageData >= 48X There is a 5% of reference with a coverageData >= 49X There is a 4.82% of reference with a coverageData >= 50X There is a 4.63% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5175481599 20.76416731976768 45.2049752676535 chr2 243199373 3179562592 13.073893048235778 43.88325712433227 chr3 198022430 2598352406 13.121505508239647 19.680657536694966 chr4 191154276 2118703950 11.08373819479717 20.148287157964706 chr5 180915260 2299846301 12.712284751435561 19.505571759294327 chr6 171115067 1514060599 8.848201537974443 19.55357126307946 chr7 159138663 2954884683 18.567987359551964 27.989652463534938 chr8 146364022 1409764245 9.631904246249805 18.464200069071246 chr9 141213431 1270899942 8.999851735066192 38.65703075676051 chr10 135534747 2051450561 15.135975138537722 43.712909422279985 chr11 135006516 2388511269 17.69182214138464 29.075620667724614 chr12 133851895 1988505477 14.856012886481734 24.638038575846366 chr13 115169878 792780196 6.883572421601419 16.534849262504956 chr14 107349540 1336046892 12.44576261807922 26.492407330271284 chr15 102531392 910762747 8.882769747239948 17.27774418706607 chr16 90354753 1434421409 15.875439435930947 39.911233461507976 chr17 81195210 1543934686 19.01509566882086 36.748464840722114 chr18 78077248 1311797698 16.801279906791798 47.85298127901723 chr19 59128983 1313361190 22.211800767823117 42.61990804399043 chr20 63025520 1107924514 17.578982513749985 28.679407070887084 chr21 48129895 501568600 10.421144696035594 24.116945149153104 chr22 51304566 971546058 18.936834160140833 43.020097215675776 chrMT 16571 6347726 383.0623378190815 131.60580188410364 chrX 155270560 609795675 3.9273103349405063 11.939942973717244 chrY 59373566 170084041 2.864642507744945 36.768974179743935