BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153400.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 = 243,865,252 number of mapped reads = 229,978,073 (94.31%) number of supplementary alignments = 168,103 (0.07%) number of secondary alignments = 0 number of mapped bases = 22,566,460,781 bp number of sequenced bases = 22,562,940,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,101,950 duplication rate = 42.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.884 >>>>>>> ACTG content number of A's = 5,700,416,872 bp (25.26%) number of C's = 5,608,316,445 bp (24.86%) number of T's = 5,616,677,948 bp (24.89%) number of G's = 5,613,173,940 bp (24.88%) number of N's = 24,355,430 bp (0.11%) GC percentage = 49.73% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 135,978,425 number of insertions = 1,096,377 mapped reads with insertion percentage = 0.46% number of deletions = 1,409,761 mapped reads with deletion percentage = 0.6% homopolymer indels = 40.03% >>>>>>> Coverage mean coverageData = 7.2896X std coverageData = 61.8869X There is a 64.34% of reference with a coverageData >= 1X There is a 42.61% of reference with a coverageData >= 2X There is a 27.45% of reference with a coverageData >= 3X There is a 17.97% of reference with a coverageData >= 4X There is a 12.39% of reference with a coverageData >= 5X There is a 9.19% of reference with a coverageData >= 6X There is a 7.38% of reference with a coverageData >= 7X There is a 6.33% of reference with a coverageData >= 8X There is a 5.71% of reference with a coverageData >= 9X There is a 5.31% of reference with a coverageData >= 10X There is a 5.05% of reference with a coverageData >= 11X There is a 4.86% of reference with a coverageData >= 12X There is a 4.71% of reference with a coverageData >= 13X There is a 4.59% of reference with a coverageData >= 14X There is a 4.49% of reference with a coverageData >= 15X There is a 4.4% of reference with a coverageData >= 16X There is a 4.32% of reference with a coverageData >= 17X There is a 4.24% of reference with a coverageData >= 18X There is a 4.18% of reference with a coverageData >= 19X There is a 4.11% of reference with a coverageData >= 20X There is a 4.05% of reference with a coverageData >= 21X There is a 4% of reference with a coverageData >= 22X There is a 3.94% of reference with a coverageData >= 23X There is a 3.89% of reference with a coverageData >= 24X There is a 3.84% of reference with a coverageData >= 25X There is a 3.8% of reference with a coverageData >= 26X There is a 3.75% of reference with a coverageData >= 27X There is a 3.71% of reference with a coverageData >= 28X There is a 3.67% of reference with a coverageData >= 29X There is a 3.62% of reference with a coverageData >= 30X There is a 3.58% of reference with a coverageData >= 31X There is a 3.55% of reference with a coverageData >= 32X There is a 3.51% of reference with a coverageData >= 33X There is a 3.47% of reference with a coverageData >= 34X There is a 3.44% of reference with a coverageData >= 35X There is a 3.4% of reference with a coverageData >= 36X There is a 3.37% of reference with a coverageData >= 37X There is a 3.34% of reference with a coverageData >= 38X There is a 3.3% of reference with a coverageData >= 39X There is a 3.27% of reference with a coverageData >= 40X There is a 3.24% of reference with a coverageData >= 41X There is a 3.21% of reference with a coverageData >= 42X There is a 3.18% of reference with a coverageData >= 43X There is a 3.15% of reference with a coverageData >= 44X There is a 3.12% of reference with a coverageData >= 45X There is a 3.09% of reference with a coverageData >= 46X There is a 3.06% of reference with a coverageData >= 47X There is a 3.04% of reference with a coverageData >= 48X There is a 3.01% of reference with a coverageData >= 49X There is a 2.98% of reference with a coverageData >= 50X There is a 2.95% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2055992385 8.248695135648228 63.21127686724131 chr2 243199373 1440730320 5.924070865100462 46.52972929419838 chr3 198022430 1129819604 5.7055132794805115 40.20679319722708 chr4 191154276 878544896 4.595999181310493 34.52071116233542 chr5 180915260 1349579575 7.459733219851106 58.088750029495344 chr6 171115067 656406028 3.8360504396728548 21.681670335680607 chr7 159138663 1214266884 7.63024434860308 102.87391397690368 chr8 146364022 1523816334 10.411140068288093 158.69995543449886 chr9 141213431 632399253 4.4783222709177 28.06358855857563 chr10 135534747 1106488894 8.163876190361723 61.183252925254536 chr11 135006516 1046493230 7.7514275681330815 37.42202862330932 chr12 133851895 922241736 6.890016282548708 31.886059400804186 chr13 115169878 276816522 2.4035496677351693 15.00127902814884 chr14 107349540 579078581 5.394327549051445 31.59947727699642 chr15 102531392 1136410439 11.083536630420467 61.593523367309565 chr16 90354753 1226695555 13.576436371864133 72.69333515336358 chr17 81195210 1054826214 12.991236970752338 72.28824273186993 chr18 78077248 251471577 3.2208048239610085 29.015745832859558 chr19 59128983 1345742548 22.759440120930204 81.35772778048687 chr20 63025520 621534172 9.861627036159321 46.265117069222555 chr21 48129895 339219973 7.0480098284029085 55.13275574713957 chr22 51304566 489660723 9.544193844267195 52.366726691409625 chrMT 16571 1921088 115.93072234626757 39.695256625857354 chrX 155270560 1224907043 7.888855704519904 43.12040169620969 chrY 59373566 61397207 1.034083197899887 50.69679929521557