BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153363.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 = 152,537,200 number of mapped reads = 148,782,368 (97.54%) number of supplementary alignments = 939,302 (0.62%) number of secondary alignments = 0 number of mapped bases = 14,586,889,696 bp number of sequenced bases = 14,584,435,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,356,598 duplication rate = 32.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4043 >>>>>>> ACTG content number of A's = 3,702,111,278 bp (25.38%) number of C's = 3,590,087,026 bp (24.62%) number of T's = 3,736,104,854 bp (25.62%) number of G's = 3,553,753,340 bp (24.37%) number of N's = 2,378,942 bp (0.02%) GC percentage = 48.98% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 56,431,725 number of insertions = 847,732 mapped reads with insertion percentage = 0.56% number of deletions = 1,103,813 mapped reads with deletion percentage = 0.73% homopolymer indels = 45.33% >>>>>>> Coverage mean coverageData = 4.712X std coverageData = 35.5523X There is a 55.99% of reference with a coverageData >= 1X There is a 37.86% of reference with a coverageData >= 2X There is a 25.45% of reference with a coverageData >= 3X There is a 18.21% of reference with a coverageData >= 4X There is a 13.59% of reference with a coverageData >= 5X There is a 10.69% of reference with a coverageData >= 6X There is a 8.76% of reference with a coverageData >= 7X There is a 7.45% of reference with a coverageData >= 8X There is a 6.52% of reference with a coverageData >= 9X There is a 5.83% of reference with a coverageData >= 10X There is a 5.31% of reference with a coverageData >= 11X There is a 4.91% of reference with a coverageData >= 12X There is a 4.58% of reference with a coverageData >= 13X There is a 4.31% of reference with a coverageData >= 14X There is a 4.08% of reference with a coverageData >= 15X There is a 3.89% of reference with a coverageData >= 16X There is a 3.72% of reference with a coverageData >= 17X There is a 3.57% of reference with a coverageData >= 18X There is a 3.43% of reference with a coverageData >= 19X There is a 3.31% of reference with a coverageData >= 20X There is a 3.2% of reference with a coverageData >= 21X There is a 3.09% of reference with a coverageData >= 22X There is a 3% of reference with a coverageData >= 23X There is a 2.91% of reference with a coverageData >= 24X There is a 2.83% of reference with a coverageData >= 25X There is a 2.75% of reference with a coverageData >= 26X There is a 2.68% of reference with a coverageData >= 27X There is a 2.61% of reference with a coverageData >= 28X There is a 2.54% of reference with a coverageData >= 29X There is a 2.48% of reference with a coverageData >= 30X There is a 2.42% of reference with a coverageData >= 31X There is a 2.37% of reference with a coverageData >= 32X There is a 2.31% of reference with a coverageData >= 33X There is a 2.26% of reference with a coverageData >= 34X There is a 2.21% of reference with a coverageData >= 35X There is a 2.16% of reference with a coverageData >= 36X There is a 2.12% of reference with a coverageData >= 37X There is a 2.07% of reference with a coverageData >= 38X There is a 2.03% of reference with a coverageData >= 39X There is a 1.99% of reference with a coverageData >= 40X There is a 1.95% of reference with a coverageData >= 41X There is a 1.91% of reference with a coverageData >= 42X There is a 1.88% of reference with a coverageData >= 43X There is a 1.84% of reference with a coverageData >= 44X There is a 1.81% of reference with a coverageData >= 45X There is a 1.77% of reference with a coverageData >= 46X There is a 1.74% of reference with a coverageData >= 47X There is a 1.71% of reference with a coverageData >= 48X There is a 1.68% of reference with a coverageData >= 49X There is a 1.65% of reference with a coverageData >= 50X There is a 1.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1416790608 5.684200915190498 35.69776090111658 chr2 243199373 899054313 3.6967789098699693 20.658162454747128 chr3 198022430 678812896 3.427959630633762 18.738303195270017 chr4 191154276 507152827 2.6531074146622804 27.649395267057894 chr5 180915260 879346930 4.860545926308261 59.707549399936866 chr6 171115067 391923026 2.290406291340785 13.783979882159835 chr7 159138663 788010962 4.951725414458207 50.23006446148706 chr8 146364022 782919055 5.349122306846692 58.33140780098332 chr9 141213431 368775812 2.611478309028551 16.39937466604898 chr10 135534747 750416266 5.53670761638711 28.022542865208163 chr11 135006516 696413782 5.1583716300033995 25.165478383957357 chr12 133851895 660465016 4.9342970900785526 24.556854202417902 chr13 115169878 159709978 1.3867339340239642 8.340697732906548 chr14 107349540 366797199 3.4168492850551573 18.918908989771765 chr15 102531392 764388821 7.455168666782559 41.7458596150101 chr16 90354753 820287932 9.078525531468168 54.61320988823883 chr17 81195210 748303906 9.216109004459746 61.17106466997582 chr18 78077248 132879245 1.7018945775342902 12.388801997486349 chr19 59128983 960226321 16.239520321193414 60.73840359309187 chr20 63025520 434004634 6.886172997858645 31.805700358863366 chr21 48129895 178036636 3.6990863163113072 30.030305644197938 chr22 51304566 365076496 7.115867542861585 43.509486787168484 chrMT 16571 151413 9.137227686922937 4.727839302863369 chrX 155270560 815925932 5.254865648710226 28.00311486641508 chrY 59373566 21019690 0.35402438182675433 15.430216990282467