BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819098.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 993,943 number of mapped reads = 904,626 (91.01%) number of supplementary alignments = 3,636 (0.37%) number of secondary alignments = 0 number of mapped bases = 53,008,299 bp number of sequenced bases = 52,991,743 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,715 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8502 >>>>>>> ACTG content number of A's = 13,591,609 bp (25.65%) number of C's = 10,461,319 bp (19.74%) number of T's = 16,419,410 bp (30.98%) number of G's = 12,518,694 bp (23.62%) number of N's = 711 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 273,528 number of insertions = 3,769 mapped reads with insertion percentage = 0.41% number of deletions = 10,093 mapped reads with deletion percentage = 1.11% homopolymer indels = 40.79% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.1832X There is a 1.59% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 5074012 0.020357068638958375 0.32121663288915403 chr2 243199373 4149673 0.01706284415461877 0.21020397895864562 chr3 198022430 2739524 0.013834412596593224 0.12501414109792774 chr4 191154276 2811213 0.014706513810865523 0.13812975902253724 chr5 180915260 2968137 0.016406227976567593 0.13558093316930145 chr6 171115067 2262461 0.0132218690011675 0.1414567757672197 chr7 159138663 2578335 0.016201813886044775 0.21142524695999004 chr8 146364022 4661606 0.031849398071337506 0.20801422837150935 chr9 141213431 2244968 0.0158976946038511 0.163061618079112 chr10 135534747 2620108 0.01933163309036907 0.18410292079934254 chr11 135006516 1958925 0.014509855213210597 0.169773839953185 chr12 133851895 2464927 0.0184153313630711 0.1433561002287256 chr13 115169878 1145099 0.009942695259258675 0.10492832330458987 chr14 107349540 1310122 0.012204262822178838 0.11791616803219901 chr15 102531392 1340688 0.013075878263702887 0.12280340283724292 chr16 90354753 1877394 0.02077803256238219 0.1580831330678336 chr17 81195210 1937925 0.023867479374706957 0.1712916204451227 chr18 78077248 1179317 0.015104489850871794 0.25205085961213114 chr19 59128983 1330168 0.02249604056271355 0.24467683908458768 chr20 63025520 1796254 0.02850042332058506 0.17926971303434416 chr21 48129895 886659 0.01842220931502136 0.15129132951730373 chr22 51304566 496347 0.00967451902818942 0.10400234008486829 chrMT 16571 3194 0.19274636413010682 0.4636550973526492 chrX 155270560 3004771 0.019351839782119677 0.15651387218180043 chrY 59373566 166472 0.002803806663726413 0.09247831401649603