BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163043.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 = 81,266,328 number of mapped reads = 79,422,387 (97.73%) number of supplementary alignments = 402,636 (0.5%) number of secondary alignments = 0 number of mapped bases = 7,501,186,932 bp number of sequenced bases = 7,500,280,456 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,210,020 duplication rate = 45.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0074 >>>>>>> ACTG content number of A's = 1,794,097,456 bp (23.92%) number of C's = 1,957,615,797 bp (26.1%) number of T's = 1,767,321,503 bp (23.56%) number of G's = 1,977,541,313 bp (26.37%) number of N's = 3,704,387 bp (0.05%) GC percentage = 52.47% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 39,482,670 number of insertions = 467,995 mapped reads with insertion percentage = 0.58% number of deletions = 408,985 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 2.4231X std coverageData = 29.0813X There is a 9.15% of reference with a coverageData >= 1X There is a 6.4% of reference with a coverageData >= 2X There is a 4.66% of reference with a coverageData >= 3X There is a 4.17% of reference with a coverageData >= 4X There is a 3.76% of reference with a coverageData >= 5X There is a 3.51% of reference with a coverageData >= 6X There is a 3.31% of reference with a coverageData >= 7X There is a 3.15% of reference with a coverageData >= 8X There is a 3% of reference with a coverageData >= 9X There is a 2.88% of reference with a coverageData >= 10X There is a 2.77% of reference with a coverageData >= 11X There is a 2.67% of reference with a coverageData >= 12X There is a 2.58% of reference with a coverageData >= 13X There is a 2.5% of reference with a coverageData >= 14X There is a 2.42% of reference with a coverageData >= 15X There is a 2.35% of reference with a coverageData >= 16X There is a 2.28% of reference with a coverageData >= 17X There is a 2.21% of reference with a coverageData >= 18X There is a 2.15% of reference with a coverageData >= 19X There is a 2.1% of reference with a coverageData >= 20X There is a 2.04% of reference with a coverageData >= 21X There is a 1.99% of reference with a coverageData >= 22X There is a 1.95% of reference with a coverageData >= 23X There is a 1.9% of reference with a coverageData >= 24X There is a 1.85% of reference with a coverageData >= 25X There is a 1.81% of reference with a coverageData >= 26X There is a 1.77% of reference with a coverageData >= 27X There is a 1.73% of reference with a coverageData >= 28X There is a 1.7% of reference with a coverageData >= 29X There is a 1.66% of reference with a coverageData >= 30X There is a 1.62% of reference with a coverageData >= 31X There is a 1.59% of reference with a coverageData >= 32X There is a 1.56% of reference with a coverageData >= 33X There is a 1.53% of reference with a coverageData >= 34X There is a 1.5% of reference with a coverageData >= 35X There is a 1.47% of reference with a coverageData >= 36X There is a 1.44% of reference with a coverageData >= 37X There is a 1.41% of reference with a coverageData >= 38X There is a 1.39% of reference with a coverageData >= 39X There is a 1.36% of reference with a coverageData >= 40X There is a 1.34% of reference with a coverageData >= 41X There is a 1.31% of reference with a coverageData >= 42X There is a 1.29% of reference with a coverageData >= 43X There is a 1.27% of reference with a coverageData >= 44X There is a 1.24% of reference with a coverageData >= 45X There is a 1.22% of reference with a coverageData >= 46X There is a 1.2% of reference with a coverageData >= 47X There is a 1.18% of reference with a coverageData >= 48X There is a 1.16% of reference with a coverageData >= 49X There is a 1.14% of reference with a coverageData >= 50X There is a 1.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1128115552 4.526029052501338 44.61646891608894 chr2 243199373 319136623 1.3122427869088298 15.90915981643027 chr3 198022430 296195161 1.4957657119953534 15.9443257995796 chr4 191154276 145281266 0.7600210104638203 11.212601680570655 chr5 180915260 369411381 2.041902827876432 30.279390629443505 chr6 171115067 431418465 2.5212184558826722 26.922217063081515 chr7 159138663 440571913 2.7684781604580904 31.237084076168276 chr8 146364022 358943872 2.452405086271816 45.36381270339473 chr9 141213431 355575385 2.5179997574026793 25.796602369416302 chr10 135534747 168136691 1.2405430690035524 13.421267147034012 chr11 135006516 422879799 3.132291770272777 28.796340354706928 chr12 133851895 200420227 1.4973282746575982 16.150740985681203 chr13 115169878 162932549 1.4147149569785946 17.040994245242658 chr14 107349540 210397994 1.9599338199306675 19.18009661813263 chr15 102531392 320719951 3.1280171344986716 26.502569090352367 chr16 90354753 364917072 4.038714731476273 34.34672959944671 chr17 81195210 244393891 3.009954540421781 24.360284688360164 chr18 78077248 119363838 1.5287915629403332 19.452585216954247 chr19 59128983 686093685 11.603339854500796 82.53837266311488 chr20 63025520 181208893 2.875166964112315 26.087504967537324 chr21 48129895 92312785 1.9179926530070344 30.251471650938363 chr22 51304566 102622251 2.000255708234624 18.985495851439627 chrMT 16571 5207 0.3142236437149237 0.719735432291618 chrX 155270560 369952529 2.382631511086197 28.232069811244017 chrY 59373566 10179952 0.17145596409014746 8.92831979485233