BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084860.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,388,337 number of mapped reads = 2,097,630 (87.83%) number of supplementary alignments = 18,117 (0.76%) number of secondary alignments = 0 number of mapped bases = 142,148,202 bp number of sequenced bases = 142,094,140 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,956 duplication rate = 5.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6864 >>>>>>> ACTG content number of A's = 40,476,261 bp (28.49%) number of C's = 25,609,926 bp (18.02%) number of T's = 45,966,462 bp (32.35%) number of G's = 30,019,788 bp (21.13%) number of N's = 21,703 bp (0.02%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,172,739 number of insertions = 10,946 mapped reads with insertion percentage = 0.52% number of deletions = 31,022 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.83% >>>>>>> Coverage mean coverageData = 0.0459X std coverageData = 0.3516X There is a 3.72% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 11023201 0.04422537025494512 0.48647323146459076 chr2 243199373 11977154 0.049248293086676664 0.3427405868255474 chr3 198022430 10021816 0.050609499136032216 0.2674661282836418 chr4 191154276 9924567 0.05191914723372445 0.27883548131367397 chr5 180915260 8808751 0.04868992809119584 0.2640853980912343 chr6 171115067 8310568 0.04856713173013572 0.26685370048178847 chr7 159138663 7443951 0.04677650835862558 0.32199249643779493 chr8 146364022 7663537 0.05235943160949758 0.7507951589186663 chr9 141213431 5895041 0.0417456112938719 0.32862174844767067 chr10 135534747 6203748 0.04577238042138375 0.30316561601612807 chr11 135006516 6872143 0.05090230607832292 0.30498773451090627 chr12 133851895 6322069 0.04723182290396412 0.262813730663319 chr13 115169878 4403736 0.03823687301292444 0.23212736157309263 chr14 107349540 4469427 0.041634337697208576 0.25411346434096327 chr15 102531392 3938524 0.03841285993659386 0.2313425104614833 chr16 90354753 3694942 0.040893720333671876 0.25510327761689755 chr17 81195210 3349521 0.04125269212309445 0.2577429256928104 chr18 78077248 4176771 0.05349536653750911 0.6260438597762764 chr19 59128983 2198885 0.037187938781223416 0.35839433504372387 chr20 63025520 2672150 0.04239790484870256 0.24751375515110358 chr21 48129895 1819636 0.037806772692938556 0.24394761910023036 chr22 51304566 1378914 0.02687702299245646 0.1905687233426559 chrMT 16571 37550 2.2660068794882626 1.8453532053333925 chrX 155270560 9215643 0.05935215922451751 0.3112828788741703 chrY 59373566 325957 0.00548993469585438 0.11027134656816169