BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153351.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 = 47,783,886 number of mapped reads = 47,463,123 (99.33%) number of supplementary alignments = 258,451 (0.54%) number of secondary alignments = 0 number of mapped bases = 4,621,183,488 bp number of sequenced bases = 4,620,628,009 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,744,209 duplication rate = 59.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.7543 >>>>>>> ACTG content number of A's = 1,221,840,016 bp (26.44%) number of C's = 1,080,974,846 bp (23.39%) number of T's = 1,255,681,368 bp (27.18%) number of G's = 1,060,766,497 bp (22.96%) number of N's = 1,365,282 bp (0.03%) GC percentage = 46.35% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 12,121,625 number of insertions = 324,234 mapped reads with insertion percentage = 0.68% number of deletions = 279,275 mapped reads with deletion percentage = 0.58% homopolymer indels = 49.77% >>>>>>> Coverage mean coverageData = 1.4928X std coverageData = 17.8553X There is a 9.54% of reference with a coverageData >= 1X There is a 6.71% of reference with a coverageData >= 2X There is a 4.58% of reference with a coverageData >= 3X There is a 3.82% of reference with a coverageData >= 4X There is a 3.04% of reference with a coverageData >= 5X There is a 2.77% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 2.27% of reference with a coverageData >= 8X There is a 2.09% of reference with a coverageData >= 9X There is a 1.99% of reference with a coverageData >= 10X There is a 1.88% of reference with a coverageData >= 11X There is a 1.8% of reference with a coverageData >= 12X There is a 1.72% of reference with a coverageData >= 13X There is a 1.66% of reference with a coverageData >= 14X There is a 1.6% of reference with a coverageData >= 15X There is a 1.54% of reference with a coverageData >= 16X There is a 1.49% of reference with a coverageData >= 17X There is a 1.44% of reference with a coverageData >= 18X There is a 1.4% of reference with a coverageData >= 19X There is a 1.36% of reference with a coverageData >= 20X There is a 1.32% of reference with a coverageData >= 21X There is a 1.28% of reference with a coverageData >= 22X There is a 1.25% of reference with a coverageData >= 23X There is a 1.22% of reference with a coverageData >= 24X There is a 1.18% of reference with a coverageData >= 25X There is a 1.15% of reference with a coverageData >= 26X There is a 1.13% of reference with a coverageData >= 27X There is a 1.1% of reference with a coverageData >= 28X There is a 1.07% of reference with a coverageData >= 29X There is a 1.05% of reference with a coverageData >= 30X There is a 1.03% of reference with a coverageData >= 31X There is a 1% of reference with a coverageData >= 32X There is a 0.98% of reference with a coverageData >= 33X There is a 0.96% of reference with a coverageData >= 34X There is a 0.94% of reference with a coverageData >= 35X There is a 0.92% of reference with a coverageData >= 36X There is a 0.9% of reference with a coverageData >= 37X There is a 0.88% of reference with a coverageData >= 38X There is a 0.86% of reference with a coverageData >= 39X There is a 0.85% of reference with a coverageData >= 40X There is a 0.83% of reference with a coverageData >= 41X There is a 0.81% of reference with a coverageData >= 42X There is a 0.8% of reference with a coverageData >= 43X There is a 0.78% of reference with a coverageData >= 44X There is a 0.77% of reference with a coverageData >= 45X There is a 0.76% of reference with a coverageData >= 46X There is a 0.74% of reference with a coverageData >= 47X There is a 0.73% of reference with a coverageData >= 48X There is a 0.72% of reference with a coverageData >= 49X There is a 0.7% of reference with a coverageData >= 50X There is a 0.69% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 448853195 1.8008107390031338 18.165286394560237 chr2 243199373 359233177 1.4771139109803544 16.06994721285816 chr3 198022430 262511892 1.3256674610042913 14.739882798746654 chr4 191154276 187364230 0.9801728421706873 12.14591504459547 chr5 180915260 320803565 1.7732255698054438 18.939889329706418 chr6 171115067 152038644 0.8885169883958846 11.595857620301517 chr7 159138663 196933690 1.237497452143355 14.410094452770998 chr8 146364022 270252492 1.8464407325455978 34.2115689455713 chr9 141213431 129656495 0.9181597960041067 10.981175179174144 chr10 135534747 220067948 1.6237013228792172 17.385838801884187 chr11 135006516 211934132 1.5698066899230256 16.383883261618788 chr12 133851895 236739115 1.7686646498355514 17.092373096478166 chr13 115169878 41619588 0.3613756367789154 5.481396967942853 chr14 107349540 134370910 1.2517138871764146 13.644272315826907 chr15 102531392 176795436 1.7243054302822691 16.480469296819027 chr16 90354753 229873186 2.5441183597723964 25.97812160847212 chr17 81195210 150012333 1.84755151196727 15.036265583481246 chr18 78077248 51312191 0.6571977408834901 8.917218397241248 chr19 59128983 234018243 3.9577586342048194 30.044586056353094 chr20 63025520 95195473 1.510427410991611 14.925543123748307 chr21 48129895 51180256 1.0633776782600501 13.149539763481476 chr22 51304566 69826989 1.3610287435235298 14.782570537384016 chrMT 16571 11483 0.6929575764890471 1.6873078896215452 chrX 155270560 387752081 2.4972672282498367 27.782615094161493 chrY 59373566 2826744 0.04760946984386958 1.9052487057035739