BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975286.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 3,515,666 number of mapped reads = 3,492,388 (99.34%) number of supplementary alignments = 9,760 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,745,801 number of mapped paired reads (second in pair) = 1,746,587 number of mapped paired reads (both in pair) = 3,485,202 number of mapped paired reads (singletons) = 7,186 number of mapped bases = 324,151,559 bp number of sequenced bases = 323,997,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,696 duplication rate = 2.35% >>>>>>> Insert size mean insert size = 58,762.9731 std insert size = 2,365,943.9238 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 53.0179 >>>>>>> ACTG content number of A's = 93,696,561 bp (28.92%) number of C's = 63,784,284 bp (19.69%) number of T's = 96,054,475 bp (29.65%) number of G's = 70,454,639 bp (21.75%) number of N's = 7,254 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 2,241,347 number of insertions = 44,115 mapped reads with insertion percentage = 1.24% number of deletions = 93,759 mapped reads with deletion percentage = 2.64% homopolymer indels = 48.21% >>>>>>> Coverage mean coverageData = 0.1047X std coverageData = 0.9086X There is a 7.34% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 30752921 0.12338152208655881 0.6456681469015348 chr2 243199373 25693969 0.1056498159639581 0.8603555738369105 chr3 198022430 24444758 0.12344438960778333 0.4831961644176375 chr4 191154276 19848548 0.10383522888078109 0.5754130963017312 chr5 180915260 19068275 0.1053989309691178 0.412619658298661 chr6 171115067 26291923 0.15365054323357744 0.6713879311952851 chr7 159138663 18312620 0.1150733558695287 0.9688040245925369 chr8 146364022 15309593 0.10459942812995396 0.45861330760909635 chr9 141213431 13433489 0.09512897537345438 1.143633913313823 chr10 135534747 17998294 0.13279468474604522 2.8458621968620177 chr11 135006516 11286186 0.08359734281269803 0.6828228922652219 chr12 133851895 14581192 0.10893526759557644 0.4201588069110466 chr13 115169878 10455759 0.09078553508583208 0.3871141078147966 chr14 107349540 10204800 0.09506142271312946 0.40730686130840005 chr15 102531392 8967065 0.08745677616470866 0.3756734444028892 chr16 90354753 11010234 0.12185561505546919 1.552831017342048 chr17 81195210 6142524 0.07565130997259567 0.5483887848475556 chr18 78077248 9188449 0.11768407872162708 1.226037629026885 chr19 59128983 3910502 0.0661351134688043 0.4298755665691828 chr20 63025520 7485183 0.11876431959625244 0.45439418381567515 chr21 48129895 3941885 0.08190096820281864 0.422110385076053 chr22 51304566 3515585 0.06852382300631878 0.3448537586037185 chrMT 16571 26694 1.6108864884436667 2.094881801860137 chrX 155270560 9729200 0.0626596567952096 0.39272450368303835 chrY 59373566 2551911 0.04298059173336498 0.7311593840109236