BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504639.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 = 398,288,092 number of mapped reads = 362,310,969 (90.97%) number of supplementary alignments = 2,830,674 (0.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 184,434,499 number of mapped paired reads (second in pair) = 177,876,470 number of mapped paired reads (both in pair) = 352,769,380 number of mapped paired reads (singletons) = 9,541,589 number of mapped bases = 30,730,910,620 bp number of sequenced bases = 30,721,910,673 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,992,765 duplication rate = 22.92% >>>>>>> Insert size mean insert size = 57,682.2711 std insert size = 2,312,898.7242 median insert size = 348 >>>>>>> Mapping quality mean mapping quality = 53.2852 >>>>>>> ACTG content number of A's = 8,106,868,715 bp (26.39%) number of C's = 7,122,116,062 bp (23.18%) number of T's = 8,145,010,672 bp (26.51%) number of G's = 7,214,420,938 bp (23.48%) number of N's = 133,494,286 bp (0.43%) GC percentage = 46.67% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 291,706,358 number of insertions = 15,017,026 mapped reads with insertion percentage = 3.14% number of deletions = 4,232,772 mapped reads with deletion percentage = 1.09% homopolymer indels = 24.64% >>>>>>> Coverage mean coverageData = 9.927X std coverageData = 22.8495X There is a 71.51% of reference with a coverageData >= 1X There is a 62.59% of reference with a coverageData >= 2X There is a 55.62% of reference with a coverageData >= 3X There is a 49.85% of reference with a coverageData >= 4X There is a 44.94% of reference with a coverageData >= 5X There is a 40.71% of reference with a coverageData >= 6X There is a 37.03% of reference with a coverageData >= 7X There is a 33.81% of reference with a coverageData >= 8X There is a 30.98% of reference with a coverageData >= 9X There is a 28.47% of reference with a coverageData >= 10X There is a 26.24% of reference with a coverageData >= 11X There is a 24.25% of reference with a coverageData >= 12X There is a 22.46% of reference with a coverageData >= 13X There is a 20.86% of reference with a coverageData >= 14X There is a 19.42% of reference with a coverageData >= 15X There is a 18.12% of reference with a coverageData >= 16X There is a 16.93% of reference with a coverageData >= 17X There is a 15.86% of reference with a coverageData >= 18X There is a 14.88% of reference with a coverageData >= 19X There is a 13.98% of reference with a coverageData >= 20X There is a 13.16% of reference with a coverageData >= 21X There is a 12.41% of reference with a coverageData >= 22X There is a 11.71% of reference with a coverageData >= 23X There is a 11.07% of reference with a coverageData >= 24X There is a 10.48% of reference with a coverageData >= 25X There is a 9.93% of reference with a coverageData >= 26X There is a 9.42% of reference with a coverageData >= 27X There is a 8.95% of reference with a coverageData >= 28X There is a 8.5% of reference with a coverageData >= 29X There is a 8.09% of reference with a coverageData >= 30X There is a 7.71% of reference with a coverageData >= 31X There is a 7.35% of reference with a coverageData >= 32X There is a 7.01% of reference with a coverageData >= 33X There is a 6.7% of reference with a coverageData >= 34X There is a 6.4% of reference with a coverageData >= 35X There is a 6.12% of reference with a coverageData >= 36X There is a 5.86% of reference with a coverageData >= 37X There is a 5.61% of reference with a coverageData >= 38X There is a 5.38% of reference with a coverageData >= 39X There is a 5.16% of reference with a coverageData >= 40X There is a 4.95% of reference with a coverageData >= 41X There is a 4.76% of reference with a coverageData >= 42X There is a 4.57% of reference with a coverageData >= 43X There is a 4.39% of reference with a coverageData >= 44X There is a 4.23% of reference with a coverageData >= 45X There is a 4.07% of reference with a coverageData >= 46X There is a 3.92% of reference with a coverageData >= 47X There is a 3.78% of reference with a coverageData >= 48X There is a 3.64% of reference with a coverageData >= 49X There is a 3.51% of reference with a coverageData >= 50X There is a 3.39% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2594724634 10.41010298626297 21.48329083798684 chr2 243199373 1720446222 7.074221453687712 17.487219956274902 chr3 198022430 1518458113 7.66811170330553 15.119646924134981 chr4 191154276 1185273509 6.20061205954922 10.975015347603478 chr5 180915260 2085214204 11.52591663080273 19.363841047069542 chr6 171115067 811226695 4.740825628172182 10.660812111830124 chr7 159138663 1577754321 9.914336913839724 16.60923385094423 chr8 146364022 1789486302 12.226271713139996 32.13438952880614 chr9 141213431 848645684 6.009666913340559 13.336674275066224 chr10 135534747 1773023712 13.081691235975082 21.786762996837478 chr11 135006516 1358889274 10.065360652666572 18.68955655256152 chr12 133851895 1472360084 10.999919605172568 23.176473488416597 chr13 115169878 400473329 3.4772401946974365 6.733991650207753 chr14 107349540 927548473 8.640451305147652 15.818108656021757 chr15 102531392 1250845979 12.199639101749442 22.889286130737556 chr16 90354753 1822609072 20.171701116818944 32.35749175879712 chr17 81195210 1359510135 16.743723367425247 29.281092457911846 chr18 78077248 415724424 5.324527114480264 44.726446243706505 chr19 59128983 1596529749 27.000798390190475 54.0020545256561 chr20 63025520 1543207730 24.485442246251996 34.81847457161103 chr21 48129895 466457518 9.691637972615565 18.828198072255113 chr22 51304566 626602613 12.213388823910917 25.963270738848625 chrMT 16571 371020 22.38971697543902 18.300811178403823 chrX 155270560 1541719707 9.929246774147012 17.829549420199744 chrY 59373566 43808117 0.7378387378652648 26.024141631356507