BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163153.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 = 80,409,386 number of mapped reads = 79,612,448 (99.01%) number of supplementary alignments = 402,500 (0.5%) number of secondary alignments = 0 number of mapped bases = 7,857,676,966 bp number of sequenced bases = 7,856,718,885 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,331,547 duplication rate = 41.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2614 >>>>>>> ACTG content number of A's = 1,907,833,903 bp (24.28%) number of C's = 2,020,506,689 bp (25.72%) number of T's = 1,914,010,467 bp (24.36%) number of G's = 2,014,106,745 bp (25.64%) number of N's = 261,081 bp (0%) GC percentage = 51.35% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 24,266,042 number of insertions = 558,113 mapped reads with insertion percentage = 0.69% number of deletions = 390,376 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 2.5383X std coverageData = 31.5685X There is a 10.23% of reference with a coverageData >= 1X There is a 6.52% of reference with a coverageData >= 2X There is a 4.89% of reference with a coverageData >= 3X There is a 4.33% of reference with a coverageData >= 4X There is a 3.93% of reference with a coverageData >= 5X There is a 3.67% of reference with a coverageData >= 6X There is a 3.45% of reference with a coverageData >= 7X There is a 3.27% of reference with a coverageData >= 8X There is a 3.12% of reference with a coverageData >= 9X There is a 2.99% of reference with a coverageData >= 10X There is a 2.87% of reference with a coverageData >= 11X There is a 2.76% of reference with a coverageData >= 12X There is a 2.66% of reference with a coverageData >= 13X There is a 2.57% of reference with a coverageData >= 14X There is a 2.49% of reference with a coverageData >= 15X There is a 2.41% of reference with a coverageData >= 16X There is a 2.34% of reference with a coverageData >= 17X There is a 2.27% of reference with a coverageData >= 18X There is a 2.21% of reference with a coverageData >= 19X There is a 2.15% of reference with a coverageData >= 20X There is a 2.09% of reference with a coverageData >= 21X There is a 2.04% of reference with a coverageData >= 22X There is a 1.99% of reference with a coverageData >= 23X There is a 1.94% of reference with a coverageData >= 24X There is a 1.89% of reference with a coverageData >= 25X There is a 1.85% of reference with a coverageData >= 26X There is a 1.8% of reference with a coverageData >= 27X There is a 1.76% of reference with a coverageData >= 28X There is a 1.72% of reference with a coverageData >= 29X There is a 1.69% of reference with a coverageData >= 30X There is a 1.65% of reference with a coverageData >= 31X There is a 1.62% of reference with a coverageData >= 32X There is a 1.58% of reference with a coverageData >= 33X There is a 1.55% of reference with a coverageData >= 34X There is a 1.52% of reference with a coverageData >= 35X There is a 1.49% of reference with a coverageData >= 36X There is a 1.46% of reference with a coverageData >= 37X There is a 1.43% of reference with a coverageData >= 38X There is a 1.41% of reference with a coverageData >= 39X There is a 1.38% of reference with a coverageData >= 40X There is a 1.35% of reference with a coverageData >= 41X There is a 1.33% of reference with a coverageData >= 42X There is a 1.31% of reference with a coverageData >= 43X There is a 1.28% of reference with a coverageData >= 44X There is a 1.26% of reference with a coverageData >= 45X There is a 1.24% of reference with a coverageData >= 46X There is a 1.22% of reference with a coverageData >= 47X There is a 1.2% of reference with a coverageData >= 48X There is a 1.18% of reference with a coverageData >= 49X There is a 1.16% of reference with a coverageData >= 50X There is a 1.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 853187006 3.4230085468874316 34.83263950642324 chr2 243199373 500169138 2.056621823609718 23.653464004776183 chr3 198022430 377935060 1.908546723722156 20.293656420178596 chr4 191154276 270590353 1.4155600317306007 20.412705721784015 chr5 180915260 397833094 2.199002416932657 36.020203290037266 chr6 171115067 400713146 2.3417759349034997 29.04473825896974 chr7 159138663 443630667 2.787698844748997 35.046863489793175 chr8 146364022 355379687 2.428053575898591 49.369292290342685 chr9 141213431 339654007 2.4052528473725703 31.12007275873893 chr10 135534747 307406639 2.26810206094235 24.51160833844028 chr11 135006516 405657544 3.004725668204044 28.45201846993008 chr12 133851895 384560208 2.873027744582921 32.67775590820225 chr13 115169878 125231302 1.08736159293318 13.821966863586637 chr14 107349540 205001797 1.909666282687378 20.943416217433246 chr15 102531392 335361881 3.2708214963081748 28.09825525767713 chr16 90354753 283153494 3.1337974439485214 29.72726724804198 chr17 81195210 395317564 4.868730113512854 39.52856062642148 chr18 78077248 122708691 1.5716318664305382 17.949608079323685 chr19 59128983 453947544 7.677242546180779 55.149705292679016 chr20 63025520 166486637 2.641574984228611 27.892152877724772 chr21 48129895 116522936 2.4210095617287344 67.45924094285269 chr22 51304566 152931304 2.980851723801737 29.33478189154621 chrMT 16571 840 0.05069096614567618 0.2878904509351491 chrX 155270560 456077102 2.93730570688996 36.07298434813744 chrY 59373566 8219325 0.13843408024372328 8.402320239388533