BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504591.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 = 365,804,720 number of mapped reads = 349,347,015 (95.5%) number of supplementary alignments = 987,043 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 174,900,303 number of mapped paired reads (second in pair) = 174,446,712 number of mapped paired reads (both in pair) = 346,621,222 number of mapped paired reads (singletons) = 2,725,793 number of mapped bases = 33,574,297,619 bp number of sequenced bases = 33,563,525,291 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,802,999 duplication rate = 18.03% >>>>>>> Insert size mean insert size = 33,349.3447 std insert size = 1,733,353.9376 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.3788 >>>>>>> ACTG content number of A's = 9,536,407,848 bp (28.41%) number of C's = 7,200,189,290 bp (21.45%) number of T's = 9,441,201,727 bp (28.13%) number of G's = 7,377,920,625 bp (21.98%) number of N's = 7,805,801 bp (0.02%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 189,242,246 number of insertions = 3,393,146 mapped reads with insertion percentage = 0.93% number of deletions = 4,168,671 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.39% >>>>>>> Coverage mean coverageData = 10.8455X std coverageData = 95.4733X There is a 90.88% of reference with a coverageData >= 1X There is a 89.13% of reference with a coverageData >= 2X There is a 86.16% of reference with a coverageData >= 3X There is a 82.02% of reference with a coverageData >= 4X There is a 76.84% of reference with a coverageData >= 5X There is a 70.91% of reference with a coverageData >= 6X There is a 64.53% of reference with a coverageData >= 7X There is a 57.99% of reference with a coverageData >= 8X There is a 51.53% of reference with a coverageData >= 9X There is a 45.35% of reference with a coverageData >= 10X There is a 39.57% of reference with a coverageData >= 11X There is a 34.3% of reference with a coverageData >= 12X There is a 29.56% of reference with a coverageData >= 13X There is a 25.36% of reference with a coverageData >= 14X There is a 21.69% of reference with a coverageData >= 15X There is a 18.52% of reference with a coverageData >= 16X There is a 15.8% of reference with a coverageData >= 17X There is a 13.48% of reference with a coverageData >= 18X There is a 11.52% of reference with a coverageData >= 19X There is a 9.87% of reference with a coverageData >= 20X There is a 8.49% of reference with a coverageData >= 21X There is a 7.33% of reference with a coverageData >= 22X There is a 6.35% of reference with a coverageData >= 23X There is a 5.54% of reference with a coverageData >= 24X There is a 4.86% of reference with a coverageData >= 25X There is a 4.29% of reference with a coverageData >= 26X There is a 3.81% of reference with a coverageData >= 27X There is a 3.41% of reference with a coverageData >= 28X There is a 3.06% of reference with a coverageData >= 29X There is a 2.77% of reference with a coverageData >= 30X There is a 2.52% of reference with a coverageData >= 31X There is a 2.31% of reference with a coverageData >= 32X There is a 2.12% of reference with a coverageData >= 33X There is a 1.96% of reference with a coverageData >= 34X There is a 1.82% of reference with a coverageData >= 35X There is a 1.7% of reference with a coverageData >= 36X There is a 1.59% of reference with a coverageData >= 37X There is a 1.49% of reference with a coverageData >= 38X There is a 1.41% of reference with a coverageData >= 39X There is a 1.33% of reference with a coverageData >= 40X There is a 1.26% of reference with a coverageData >= 41X There is a 1.19% of reference with a coverageData >= 42X There is a 1.14% of reference with a coverageData >= 43X There is a 1.08% of reference with a coverageData >= 44X There is a 1.03% of reference with a coverageData >= 45X There is a 0.99% of reference with a coverageData >= 46X There is a 0.94% of reference with a coverageData >= 47X There is a 0.91% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.84% of reference with a coverageData >= 50X There is a 0.8% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3122278716 12.526663738984226 172.94869853195343 chr2 243199373 2372060075 9.753561638499784 57.465450769016556 chr3 198022430 1986844394 10.033431031020072 16.710815627013037 chr4 191154276 1903182744 9.956265608204339 114.7949278914929 chr5 180915260 1585309682 8.762719529574232 10.367300417235676 chr6 171115067 1572861632 9.191835994196817 22.61253584721257 chr7 159138663 2833546091 17.80551650732418 137.52434991532928 chr8 146364022 2952517737 20.17242828295604 67.36859447190595 chr9 141213431 1210085101 8.569192692442973 60.9746326478081 chr10 135534747 1634744388 12.06144124797754 258.8746431338626 chr11 135006516 1441668847 10.678513080064965 38.70062907029278 chr12 133851895 1254518112 9.3724344507786 8.623227868025783 chr13 115169878 814890143 7.075549242137775 6.398460493257367 chr14 107349540 1088456648 10.139369465393145 9.477274943563323 chr15 102531392 877597442 8.559304861480863 7.180070723136498 chr16 90354753 932263314 10.317811548884428 73.47859959830242 chr17 81195210 1040714224 12.817433737778375 45.17584464194305 chr18 78077248 571984970 7.325885384689788 94.28474572274503 chr19 59128983 671218366 11.351765782949455 89.15025202306398 chr20 63025520 1411146793 22.390085682752 29.084615000836624 chr21 48129895 402354264 8.35975777632592 40.016834891665724 chr22 51304566 453155482 8.832654037069528 9.425650896620825 chrMT 16571 120129485 7249.380544324422 1533.8510205965608 chrX 155270560 1191795981 7.67560818354748 18.72250330130392 chrY 59373566 128972988 2.172229102762667 116.61182015757937