BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975334.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 = 4,126,746 number of mapped reads = 4,016,423 (97.33%) number of supplementary alignments = 19,296 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,007,206 number of mapped paired reads (second in pair) = 2,009,217 number of mapped paired reads (both in pair) = 3,995,010 number of mapped paired reads (singletons) = 21,413 number of mapped bases = 367,316,348 bp number of sequenced bases = 367,103,707 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 211,941 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 79,864.0767 std insert size = 2,693,411.8736 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 52.788 >>>>>>> ACTG content number of A's = 106,103,959 bp (28.9%) number of C's = 72,596,804 bp (19.78%) number of T's = 109,687,828 bp (29.88%) number of G's = 78,707,839 bp (21.44%) number of N's = 7,277 bp (0%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 2,777,281 number of insertions = 55,681 mapped reads with insertion percentage = 1.34% number of deletions = 119,380 mapped reads with deletion percentage = 2.91% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.1187X std coverageData = 1.3539X There is a 8.35% of reference with a coverageData >= 1X There is a 2.29% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.14% 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 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 27993183 0.11230938116699818 1.4547073070382022 chr2 243199373 32739116 0.13461842272101582 1.6351296590886295 chr3 198022430 22723682 0.11475307115461617 0.43322117805314286 chr4 191154276 23242845 0.12159207466538703 0.9233437650093005 chr5 180915260 21283763 0.11764492945481769 0.45685499527152634 chr6 171115067 30423459 0.17779532529417763 1.874898038028168 chr7 159138663 19138412 0.12026249083165919 1.5482220797564645 chr8 146364022 17803376 0.12163765218203693 0.5973500206235088 chr9 141213431 16166790 0.11448479004805145 1.9606279127704997 chr10 135534747 19034494 0.14043995669981219 2.368430799035998 chr11 135006516 15620409 0.11570114882455007 0.9676015289449614 chr12 133851895 16534727 0.12353001800983095 2.1341759746556184 chr13 115169878 11174322 0.09702469251552043 0.3888760422441121 chr14 107349540 11001885 0.10248655932759469 0.446164943638297 chr15 102531392 10163723 0.09912791391732982 0.39435330870104907 chr16 90354753 11664246 0.12909388397088528 1.5854299576404183 chr17 81195210 8274706 0.10191125806559279 1.8219351782153859 chr18 78077248 15059180 0.19287539437865434 2.159299387574624 chr19 59128983 4810389 0.08135416433595687 0.8625438526314222 chr20 63025520 7699576 0.1221660051356974 0.4888893642249199 chr21 48129895 4639938 0.09640449039001643 0.5764075491250804 chr22 51304566 3470132 0.06763787846875072 0.3558336164680364 chrMT 16571 89056 5.374207953653974 4.41138544941209 chrX 155270560 13168419 0.08480950284458302 0.5659360247188251 chrY 59373566 3396520 0.057205928981931116 1.5072314141946752