BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153330.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 = 56,190,624 number of mapped reads = 55,694,819 (99.12%) number of supplementary alignments = 442,327 (0.79%) number of secondary alignments = 0 number of mapped bases = 5,407,181,796 bp number of sequenced bases = 5,406,270,007 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,929,029 duplication rate = 34.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.3717 >>>>>>> ACTG content number of A's = 1,459,549,114 bp (27%) number of C's = 1,236,430,953 bp (22.87%) number of T's = 1,490,436,308 bp (27.57%) number of G's = 1,218,260,557 bp (22.53%) number of N's = 1,593,075 bp (0.03%) GC percentage = 45.4% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 15,534,493 number of insertions = 582,825 mapped reads with insertion percentage = 1.03% number of deletions = 439,169 mapped reads with deletion percentage = 0.78% homopolymer indels = 49.57% >>>>>>> Coverage mean coverageData = 1.7467X std coverageData = 18.9307X There is a 22.23% of reference with a coverageData >= 1X There is a 11.73% of reference with a coverageData >= 2X There is a 6.61% of reference with a coverageData >= 3X There is a 4.84% of reference with a coverageData >= 4X There is a 3.78% of reference with a coverageData >= 5X There is a 3.23% of reference with a coverageData >= 6X There is a 2.86% of reference with a coverageData >= 7X There is a 2.61% of reference with a coverageData >= 8X There is a 2.41% of reference with a coverageData >= 9X There is a 2.25% of reference with a coverageData >= 10X There is a 2.12% of reference with a coverageData >= 11X There is a 2.01% of reference with a coverageData >= 12X There is a 1.92% of reference with a coverageData >= 13X There is a 1.83% of reference with a coverageData >= 14X There is a 1.75% of reference with a coverageData >= 15X There is a 1.68% of reference with a coverageData >= 16X There is a 1.61% of reference with a coverageData >= 17X There is a 1.55% of reference with a coverageData >= 18X There is a 1.5% of reference with a coverageData >= 19X There is a 1.45% of reference with a coverageData >= 20X There is a 1.4% of reference with a coverageData >= 21X There is a 1.35% of reference with a coverageData >= 22X There is a 1.31% of reference with a coverageData >= 23X There is a 1.27% of reference with a coverageData >= 24X There is a 1.23% of reference with a coverageData >= 25X There is a 1.2% of reference with a coverageData >= 26X There is a 1.16% of reference with a coverageData >= 27X There is a 1.13% of reference with a coverageData >= 28X There is a 1.1% of reference with a coverageData >= 29X There is a 1.07% of reference with a coverageData >= 30X There is a 1.05% of reference with a coverageData >= 31X There is a 1.02% of reference with a coverageData >= 32X There is a 0.99% of reference with a coverageData >= 33X There is a 0.97% of reference with a coverageData >= 34X There is a 0.95% of reference with a coverageData >= 35X There is a 0.93% 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 0.84% 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 0.79% of reference with a coverageData >= 43X There is a 0.78% of reference with a coverageData >= 44X There is a 0.76% of reference with a coverageData >= 45X There is a 0.74% of reference with a coverageData >= 46X There is a 0.73% of reference with a coverageData >= 47X There is a 0.72% of reference with a coverageData >= 48X There is a 0.7% of reference with a coverageData >= 49X There is a 0.69% of reference with a coverageData >= 50X There is a 0.67% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 559269249 2.2438028308864273 22.136394262043492 chr2 243199373 408213603 1.6785142081760218 18.613227594378234 chr3 198022430 277478198 1.4012463032596862 13.50583606055758 chr4 191154276 253132579 1.3242318419285584 14.296965918484013 chr5 180915260 354267646 1.9581965943613602 19.852336818803604 chr6 171115067 202709519 1.1846386326693255 13.642895873434517 chr7 159138663 273830197 1.7207018824834541 21.07336581520633 chr8 146364022 338175064 2.310506771944269 24.662018729145554 chr9 141213431 115610788 0.8186954114867445 9.18745841114279 chr10 135534747 238332775 1.7584625365479156 16.418414307782452 chr11 135006516 256834120 1.902383141270011 17.530747988221556 chr12 133851895 267525536 1.99866827436399 16.875600713987502 chr13 115169878 73008794 0.6339226477256492 7.3678107421851875 chr14 107349540 163784342 1.5257107016946696 14.2041406378417 chr15 102531392 240679258 2.3473714079684007 23.5533567273635 chr16 90354753 231354536 2.5605131807509895 26.818005077901855 chr17 81195210 180379967 2.22155921513104 20.14402716775503 chr18 78077248 60685439 0.7772486934990331 8.686844989525596 chr19 59128983 249874715 4.22592614183809 43.39372141356789 chr20 63025520 127582479 2.0242987126484637 17.257266228778935 chr21 48129895 60687913 1.260919289352283 14.879648253641182 chr22 51304566 63854553 1.2446173504323181 12.267347662962482 chrMT 16571 23419 1.4132520668637982 4.81140112283868 chrX 155270560 405662502 2.612616982897466 25.12294961787371 chrY 59373566 4224605 0.0711529605616075 2.7024107200914633