BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038410.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 11,158,768 number of mapped reads = 10,878,410 (97.49%) number of supplementary alignments = 230,561 (2.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,504,174 number of mapped paired reads (second in pair) = 5,374,236 number of mapped paired reads (both in pair) = 10,733,662 number of mapped paired reads (singletons) = 144,748 number of mapped bases = 1,543,920,543 bp number of sequenced bases = 1,542,724,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,645,048 duplication rate = 8.32% >>>>>>> Insert size mean insert size = 99,543.2378 std insert size = 2,920,132.74 median insert size = 265 >>>>>>> Mapping quality mean mapping quality = 53.665 >>>>>>> ACTG content number of A's = 456,681,099 bp (29.6%) number of C's = 305,825,464 bp (19.82%) number of T's = 458,743,407 bp (29.74%) number of G's = 321,442,559 bp (20.84%) number of N's = 32,046 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.015 number of mismatches = 22,253,020 number of insertions = 292,679 mapped reads with insertion percentage = 2.51% number of deletions = 543,177 mapped reads with deletion percentage = 4.78% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.4987X std coverageData = 8.7713X There is a 23.47% of reference with a coverageData >= 1X There is a 10.98% of reference with a coverageData >= 2X There is a 5.05% of reference with a coverageData >= 3X There is a 2.62% of reference with a coverageData >= 4X There is a 1.36% of reference with a coverageData >= 5X There is a 0.75% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 92575964 0.3714171849545763 8.597062691838703 chr2 243199373 135989141 0.5591673174256087 8.94631364499983 chr3 198022430 102999311 0.5201396175170662 1.2543635774155706 chr4 191154276 97429211 0.509688891291137 8.456573202995123 chr5 180915260 104991483 0.5803351414358302 1.3436469698533735 chr6 171115067 84055296 0.49122089289775983 7.924166848435187 chr7 159138663 103163312 0.6482605173074755 8.113892966047048 chr8 146364022 69682721 0.4760918704461401 2.0206336955280193 chr9 141213431 62281938 0.44104825977919904 11.38141015419805 chr10 135534747 72635553 0.5359183132573376 25.415283024605063 chr11 135006516 75759826 0.5611568111275459 5.054368795346097 chr12 133851895 53718294 0.4013263614982814 1.040132802528601 chr13 115169878 98065019 0.8514814871992832 1.6315729049198198 chr14 107349540 28406398 0.2646159266262343 0.9159770221848234 chr15 102531392 25739108 0.25103636552598446 0.7577277739763321 chr16 90354753 67726431 0.7495613540108953 16.960410751538983 chr17 81195210 33144745 0.4082105951816616 3.4572100952350238 chr18 78077248 25005584 0.3202672307302634 9.488713300164777 chr19 59128983 16881464 0.2855023567714669 4.648207341408076 chr20 63025520 53049090 0.8417080890407568 2.9693661783084373 chr21 48129895 13906855 0.2889442206345973 3.7359525337148667 chr22 51304566 7937082 0.15470517770289685 0.7652205503338323 chrMT 16571 1122723 67.75227807615714 34.97985652746674 chrX 155270560 79868475 0.5143826041459502 1.6552902765358724 chrY 59373566 37785519 0.6364030585597638 16.99615275084531