BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618576.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 58,522,558 number of mapped reads = 56,620,456 (96.75%) number of supplementary alignments = 61,632 (0.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,546,883 number of mapped paired reads (second in pair) = 28,073,573 number of mapped paired reads (both in pair) = 55,584,654 number of mapped paired reads (singletons) = 1,035,802 number of mapped bases = 5,446,414,132 bp number of sequenced bases = 5,442,996,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,246,873 duplication rate = 20.92% >>>>>>> Insert size mean insert size = 23,818.1317 std insert size = 1,539,535.9383 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 54.0215 >>>>>>> ACTG content number of A's = 1,459,314,749 bp (26.81%) number of C's = 1,244,149,438 bp (22.86%) number of T's = 1,460,508,303 bp (26.83%) number of G's = 1,278,797,422 bp (23.49%) number of N's = 226,364 bp (0%) GC percentage = 46.35% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 68,980,651 number of insertions = 939,958 mapped reads with insertion percentage = 1.64% number of deletions = 2,491,355 mapped reads with deletion percentage = 4.3% homopolymer indels = 52.46% >>>>>>> Coverage mean coverageData = 1.7594X std coverageData = 7.176X There is a 26.66% of reference with a coverageData >= 1X There is a 19.06% of reference with a coverageData >= 2X There is a 14.63% of reference with a coverageData >= 3X There is a 11.79% of reference with a coverageData >= 4X There is a 9.74% of reference with a coverageData >= 5X There is a 8.23% of reference with a coverageData >= 6X There is a 7.06% of reference with a coverageData >= 7X There is a 6.13% of reference with a coverageData >= 8X There is a 5.38% of reference with a coverageData >= 9X There is a 4.76% of reference with a coverageData >= 10X There is a 4.24% of reference with a coverageData >= 11X There is a 3.8% of reference with a coverageData >= 12X There is a 3.42% of reference with a coverageData >= 13X There is a 3.1% of reference with a coverageData >= 14X There is a 2.82% of reference with a coverageData >= 15X There is a 2.58% of reference with a coverageData >= 16X There is a 2.36% of reference with a coverageData >= 17X There is a 2.17% of reference with a coverageData >= 18X There is a 2% of reference with a coverageData >= 19X There is a 1.85% of reference with a coverageData >= 20X There is a 1.71% of reference with a coverageData >= 21X There is a 1.59% of reference with a coverageData >= 22X There is a 1.48% of reference with a coverageData >= 23X There is a 1.38% of reference with a coverageData >= 24X There is a 1.29% of reference with a coverageData >= 25X There is a 1.2% of reference with a coverageData >= 26X There is a 1.13% of reference with a coverageData >= 27X There is a 1.06% of reference with a coverageData >= 28X There is a 0.99% of reference with a coverageData >= 29X There is a 0.93% of reference with a coverageData >= 30X There is a 0.88% of reference with a coverageData >= 31X There is a 0.83% of reference with a coverageData >= 32X There is a 0.78% of reference with a coverageData >= 33X There is a 0.74% of reference with a coverageData >= 34X There is a 0.7% of reference with a coverageData >= 35X There is a 0.66% of reference with a coverageData >= 36X There is a 0.63% of reference with a coverageData >= 37X There is a 0.6% of reference with a coverageData >= 38X There is a 0.57% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.51% of reference with a coverageData >= 41X There is a 0.49% of reference with a coverageData >= 42X There is a 0.47% of reference with a coverageData >= 43X There is a 0.44% of reference with a coverageData >= 44X There is a 0.42% of reference with a coverageData >= 45X There is a 0.4% of reference with a coverageData >= 46X There is a 0.38% of reference with a coverageData >= 47X There is a 0.37% of reference with a coverageData >= 48X There is a 0.35% of reference with a coverageData >= 49X There is a 0.34% of reference with a coverageData >= 50X There is a 0.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 492689557 1.9766833680225815 8.195771956629166 chr2 243199373 433854253 1.7839447842655416 7.2495443767685925 chr3 198022430 330828421 1.670661353867842 6.032124183203276 chr4 191154276 242905206 1.2707286024823217 6.061554998542919 chr5 180915260 283917675 1.5693406681116895 5.797256923134367 chr6 171115067 273639442 1.599154573571245 5.9579336819274 chr7 159138663 262753829 1.6510998901630838 6.192570665260682 chr8 146364022 253364659 1.7310583266152662 6.275009750437587 chr9 141213431 244365521 1.7304693984809418 7.743315123354703 chr10 135534747 285949215 2.1097852862779165 7.548943807245735 chr11 135006516 285732093 2.116431869110673 8.237279775777388 chr12 133851895 246540304 1.8418887831210757 6.708553287029577 chr13 115169878 132135540 1.147309889483429 4.6915287637354455 chr14 107349540 171666995 1.5991404807137506 6.685854354461084 chr15 102531392 187969966 1.8332918566052434 6.910964881585462 chr16 90354753 205533305 2.274737057828048 10.175982510977635 chr17 81195210 201974186 2.4875135614527015 8.69071819435729 chr18 78077248 138489091 1.773744522860232 7.8351571810727805 chr19 59128983 133384595 2.2558242714913597 8.9444079705886 chr20 63025520 173745557 2.756749281878198 9.066623793452347 chr21 48129895 71572249 1.487064307952469 11.603436115077676 chr22 51304566 122432161 2.386379430633913 9.370723748958246 chrMT 16571 1192 0.07193289481624525 0.422169414302622 chrX 155270560 263964889 1.7000317961112525 6.150051193163523 chrY 59373566 7004231 0.11796884492334518 2.9066503426288888