BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053617.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 = 8,449,289 number of mapped reads = 7,186,918 (85.06%) number of supplementary alignments = 280 (0%) number of secondary alignments = 0 number of mapped bases = 339,606,054 bp number of sequenced bases = 339,542,076 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,411,788 duplication rate = 14.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5866 >>>>>>> ACTG content number of A's = 98,633,363 bp (29.05%) number of C's = 67,568,478 bp (19.9%) number of T's = 99,254,854 bp (29.23%) number of G's = 74,077,547 bp (21.82%) number of N's = 7,834 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,703,688 number of insertions = 13,232 mapped reads with insertion percentage = 0.18% number of deletions = 42,702 mapped reads with deletion percentage = 0.59% homopolymer indels = 46.34% >>>>>>> Coverage mean coverageData = 0.1097X std coverageData = 0.7953X There is a 5.19% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 1.12% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% 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 0.02% 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 0.01% 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 0.01% 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% 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 27048924 0.10852098940206853 0.8431057957716992 chr2 243199373 28552834 0.11740504775067821 1.0047683106616707 chr3 198022430 23139043 0.11685061636704488 0.7477194716664258 chr4 191154276 21801162 0.11405008800326287 0.7787875127580886 chr5 180915260 21095331 0.1166033810525436 0.7493460293092613 chr6 171115067 19800205 0.11571280862134718 0.7914944803322062 chr7 159138663 18265828 0.1147793229857662 0.8285615056290377 chr8 146364022 17035564 0.11639174550696618 0.8085536458976784 chr9 141213431 14039172 0.09941810704960494 0.7255802337025624 chr10 135534747 15874889 0.11712781667715069 0.8183556573086815 chr11 135006516 15452004 0.11445376458718481 0.8308035426664754 chr12 133851895 15635922 0.11681509626740809 0.7582775713282299 chr13 115169878 11003505 0.09554151824316424 0.6753494354200728 chr14 107349540 10392804 0.09681274833595002 0.7718282550063672 chr15 102531392 9810474 0.09568263737217184 0.6692406026083025 chr16 90354753 9772463 0.10815660134669396 0.7583446750765831 chr17 81195210 9132407 0.11247470140172063 0.7321336113829633 chr18 78077248 8944767 0.11456304146375651 0.8369080411769073 chr19 59128983 6467559 0.10938052156249668 0.8309294822376796 chr20 63025520 7292500 0.11570709769629826 0.765339400477274 chr21 48129895 4407363 0.09157225462469844 0.7989177557236491 chr22 51304566 3955625 0.07710083737965935 0.6309498508849001 chrMT 16571 113465 6.8472029449037475 11.89988703082535 chrX 155270560 19755219 0.12723093804775354 0.839023416015996 chrY 59373566 817025 0.013760753396553612 0.292047212783339