BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504601.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 = 423,713,276 number of mapped reads = 364,698,182 (86.07%) number of supplementary alignments = 2,003,393 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,646,858 number of mapped paired reads (second in pair) = 182,051,324 number of mapped paired reads (both in pair) = 362,690,082 number of mapped paired reads (singletons) = 2,008,100 number of mapped bases = 36,209,178,582 bp number of sequenced bases = 36,199,799,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,739,623 duplication rate = 21.71% >>>>>>> Insert size mean insert size = 29,242.0125 std insert size = 1,659,578.2014 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.9771 >>>>>>> ACTG content number of A's = 9,548,853,620 bp (26.38%) number of C's = 8,471,926,180 bp (23.4%) number of T's = 9,580,590,267 bp (26.47%) number of G's = 8,591,518,747 bp (23.73%) number of N's = 6,910,494 bp (0.02%) GC percentage = 47.14% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 192,610,664 number of insertions = 2,722,270 mapped reads with insertion percentage = 0.73% number of deletions = 3,642,898 mapped reads with deletion percentage = 0.97% homopolymer indels = 40.43% >>>>>>> Coverage mean coverageData = 11.6966X std coverageData = 24.1854X There is a 78.45% of reference with a coverageData >= 1X There is a 69.81% of reference with a coverageData >= 2X There is a 62.51% of reference with a coverageData >= 3X There is a 56.41% of reference with a coverageData >= 4X There is a 51.16% of reference with a coverageData >= 5X There is a 46.62% of reference with a coverageData >= 6X There is a 42.65% of reference with a coverageData >= 7X There is a 39.15% of reference with a coverageData >= 8X There is a 36.05% of reference with a coverageData >= 9X There is a 33.3% of reference with a coverageData >= 10X There is a 30.83% of reference with a coverageData >= 11X There is a 28.61% of reference with a coverageData >= 12X There is a 26.62% of reference with a coverageData >= 13X There is a 24.81% of reference with a coverageData >= 14X There is a 23.17% of reference with a coverageData >= 15X There is a 21.67% of reference with a coverageData >= 16X There is a 20.31% of reference with a coverageData >= 17X There is a 19.06% of reference with a coverageData >= 18X There is a 17.91% of reference with a coverageData >= 19X There is a 16.86% of reference with a coverageData >= 20X There is a 15.89% of reference with a coverageData >= 21X There is a 14.99% of reference with a coverageData >= 22X There is a 14.17% of reference with a coverageData >= 23X There is a 13.4% of reference with a coverageData >= 24X There is a 12.69% of reference with a coverageData >= 25X There is a 12.03% of reference with a coverageData >= 26X There is a 11.41% of reference with a coverageData >= 27X There is a 10.84% of reference with a coverageData >= 28X There is a 10.31% of reference with a coverageData >= 29X There is a 9.81% of reference with a coverageData >= 30X There is a 9.34% of reference with a coverageData >= 31X There is a 8.9% of reference with a coverageData >= 32X There is a 8.49% of reference with a coverageData >= 33X There is a 8.11% of reference with a coverageData >= 34X There is a 7.75% of reference with a coverageData >= 35X There is a 7.41% of reference with a coverageData >= 36X There is a 7.09% of reference with a coverageData >= 37X There is a 6.78% of reference with a coverageData >= 38X There is a 6.5% of reference with a coverageData >= 39X There is a 6.23% of reference with a coverageData >= 40X There is a 5.97% of reference with a coverageData >= 41X There is a 5.73% of reference with a coverageData >= 42X There is a 5.51% of reference with a coverageData >= 43X There is a 5.29% of reference with a coverageData >= 44X There is a 5.09% of reference with a coverageData >= 45X There is a 4.89% of reference with a coverageData >= 46X There is a 4.71% of reference with a coverageData >= 47X There is a 4.53% of reference with a coverageData >= 48X There is a 4.37% of reference with a coverageData >= 49X There is a 4.21% of reference with a coverageData >= 50X There is a 4.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3715881565 14.908213869605564 25.143959031451057 chr2 243199373 2483259994 10.21079932636175 18.248127269845625 chr3 198022430 2682998619 13.548963210884747 22.37855982780164 chr4 191154276 1517206628 7.93707919983961 12.579889452336703 chr5 180915260 1474048639 8.147729710583839 13.701235415574653 chr6 171115067 1851131424 10.818050429188682 17.63165892633566 chr7 159138663 2946151784 18.513111323550582 27.516084643148467 chr8 146364022 2764968033 18.891036165978 46.41419708090691 chr9 141213431 1423928649 10.08352136844547 19.682320597291874 chr10 135534747 1704303035 12.574657589466707 23.75169612856296 chr11 135006516 1845947524 13.673025411603096 23.181518456288604 chr12 133851895 1234860593 9.225574228889325 15.479683117716041 chr13 115169878 823053547 7.146430657849616 13.402399584976008 chr14 107349540 1209512763 11.267051195561713 19.574930440599914 chr15 102531392 806765702 7.868475071517609 14.723570722868415 chr16 90354753 1056660929 11.694580461085428 20.085277484733933 chr17 81195210 1311128592 16.14785640680035 49.627910895535905 chr18 78077248 473602350 6.0658176630405825 28.35817975100855 chr19 59128983 1064456692 18.002283110467165 31.255181394233148 chr20 63025520 1628265926 25.835025653100523 38.53597449966418 chr21 48129895 343581419 7.138628060584798 18.058549096722007 chr22 51304566 743719293 14.496161862084556 26.949127662432883 chrMT 16571 232586 14.035725061855048 10.983098238805898 chrX 155270560 1066990740 6.8718161382299385 12.119046589985722 chrY 59373566 36521556 0.615114746518678 14.658169739934504