BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054574.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 10,079,505 number of mapped reads = 7,586,461 (75.27%) number of supplementary alignments = 255 (0%) number of secondary alignments = 0 number of mapped bases = 359,232,934 bp number of sequenced bases = 359,162,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,938,869 duplication rate = 19.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3841 >>>>>>> ACTG content number of A's = 104,311,881 bp (29.04%) number of C's = 70,810,715 bp (19.72%) number of T's = 105,702,424 bp (29.43%) number of G's = 78,226,326 bp (21.78%) number of N's = 111,370 bp (0.03%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,873,069 number of insertions = 14,426 mapped reads with insertion percentage = 0.19% number of deletions = 46,522 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.03% >>>>>>> Coverage mean coverageData = 0.116X std coverageData = 0.9023X There is a 4.79% of reference with a coverageData >= 1X There is a 2.18% of reference with a coverageData >= 2X There is a 1.27% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% 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 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 29756715 0.11938471760116498 0.9528788018823949 chr2 243199373 36045143 0.14821231878751595 1.2257856042668935 chr3 198022430 22839702 0.11533896437893425 0.8281200981242882 chr4 191154276 16908437 0.08845440109328237 0.7211888499930847 chr5 180915260 19196286 0.10610650533293875 0.7818971390385615 chr6 171115067 21525125 0.1257932768714049 0.9137804200219929 chr7 159138663 17552377 0.11029611955455476 0.8857123691918962 chr8 146364022 19539916 0.13350217992779673 0.9531748510670895 chr9 141213431 24328259 0.1722800644932988 1.1490705409642998 chr10 135534747 12530449 0.09245193042637251 0.7677393107928662 chr11 135006516 16835929 0.12470456611146087 0.9053871390232766 chr12 133851895 18818262 0.14059017991489772 0.9339116381548369 chr13 115169878 9530436 0.08275111657233847 0.7048815379134131 chr14 107349540 6827360 0.06359934099391576 0.7136553738417675 chr15 102531392 8760063 0.08543786277669965 0.6822363262788875 chr16 90354753 9063496 0.10031011871616759 0.7893590214633358 chr17 81195210 9139473 0.11256172623976217 0.8256143558813636 chr18 78077248 12439660 0.15932503153799682 1.1021810088572253 chr19 59128983 7788593 0.1317220862736638 0.9794115038583169 chr20 63025520 7858131 0.1246817320983627 0.8861173178385815 chr21 48129895 4003470 0.08318052636516245 0.7439791493670623 chr22 51304566 5216022 0.1016677930771308 0.8043353928602471 chrMT 16571 25683 1.5498762899040492 2.990495749351603 chrX 155270560 21843143 0.14067794306918194 0.9754355619501931 chrY 59373566 860804 0.01449810173099591 0.3098421566304087