BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514731.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 42,344,547 number of mapped reads = 41,339,457 (97.63%) number of supplementary alignments = 1,176,919 (2.78%) number of secondary alignments = 0 number of mapped bases = 3,943,916,123 bp number of sequenced bases = 3,941,704,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,574,329 duplication rate = 34.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2349 >>>>>>> ACTG content number of A's = 1,001,746,051 bp (25.41%) number of C's = 951,288,963 bp (24.13%) number of T's = 1,013,233,325 bp (25.71%) number of G's = 952,346,203 bp (24.16%) number of N's = 23,090,442 bp (0.59%) GC percentage = 48.29% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 37,179,376 number of insertions = 1,423,636 mapped reads with insertion percentage = 3.32% number of deletions = 1,106,987 mapped reads with deletion percentage = 2.6% homopolymer indels = 45.24% >>>>>>> Coverage mean coverageData = 1.274X std coverageData = 30.5365X There is a 7.16% of reference with a coverageData >= 1X There is a 4.75% of reference with a coverageData >= 2X There is a 3.72% of reference with a coverageData >= 3X There is a 3.15% of reference with a coverageData >= 4X There is a 2.75% of reference with a coverageData >= 5X There is a 2.45% of reference with a coverageData >= 6X There is a 2.22% of reference with a coverageData >= 7X There is a 2.02% of reference with a coverageData >= 8X There is a 1.87% of reference with a coverageData >= 9X There is a 1.73% of reference with a coverageData >= 10X There is a 1.61% of reference with a coverageData >= 11X There is a 1.51% of reference with a coverageData >= 12X There is a 1.42% of reference with a coverageData >= 13X There is a 1.34% of reference with a coverageData >= 14X There is a 1.27% of reference with a coverageData >= 15X There is a 1.21% of reference with a coverageData >= 16X There is a 1.15% of reference with a coverageData >= 17X There is a 1.1% of reference with a coverageData >= 18X There is a 1.05% of reference with a coverageData >= 19X There is a 1% of reference with a coverageData >= 20X There is a 0.96% of reference with a coverageData >= 21X There is a 0.92% of reference with a coverageData >= 22X There is a 0.89% of reference with a coverageData >= 23X There is a 0.85% of reference with a coverageData >= 24X There is a 0.82% of reference with a coverageData >= 25X There is a 0.79% of reference with a coverageData >= 26X There is a 0.76% of reference with a coverageData >= 27X There is a 0.74% of reference with a coverageData >= 28X There is a 0.72% of reference with a coverageData >= 29X There is a 0.69% of reference with a coverageData >= 30X There is a 0.67% of reference with a coverageData >= 31X There is a 0.65% of reference with a coverageData >= 32X There is a 0.63% of reference with a coverageData >= 33X There is a 0.61% of reference with a coverageData >= 34X There is a 0.6% of reference with a coverageData >= 35X There is a 0.58% of reference with a coverageData >= 36X There is a 0.56% of reference with a coverageData >= 37X There is a 0.55% of reference with a coverageData >= 38X There is a 0.54% of reference with a coverageData >= 39X There is a 0.52% of reference with a coverageData >= 40X There is a 0.51% of reference with a coverageData >= 41X There is a 0.5% of reference with a coverageData >= 42X There is a 0.48% of reference with a coverageData >= 43X There is a 0.47% of reference with a coverageData >= 44X There is a 0.46% of reference with a coverageData >= 45X There is a 0.45% of reference with a coverageData >= 46X There is a 0.44% of reference with a coverageData >= 47X There is a 0.43% of reference with a coverageData >= 48X There is a 0.42% of reference with a coverageData >= 49X There is a 0.42% of reference with a coverageData >= 50X There is a 0.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 325687034 1.3066648848991234 16.264241532255692 chr2 243199373 230808339 0.9490498933153089 17.915530686025228 chr3 198022430 212288192 1.0720411420059839 23.2409957497939 chr4 191154276 99192954 0.5189156950901794 8.794546333213518 chr5 180915260 186128686 1.028816949990841 42.37889262591709 chr6 171115067 101410657 0.5926459824838218 22.358986684898998 chr7 159138663 109949412 0.6909032030764265 9.74417934881451 chr8 146364022 104786084 0.7159278801452996 9.101639536995828 chr9 141213431 94121231 0.6665175566763193 13.111767594492836 chr10 135534747 388698857 2.8678908221225368 46.54098746912479 chr11 135006516 103202237 0.7644241186106898 15.282513125989588 chr12 133851895 115231471 0.860887856686676 37.091419760667755 chr13 115169878 37871750 0.3288338119104372 9.26832656274769 chr14 107349540 107524060 1.0016257172597107 14.673451465448425 chr15 102531392 55067346 0.5370779126845366 9.888688886352904 chr16 90354753 245526055 2.7173562745503825 56.42632310675217 chr17 81195210 149510407 1.8413697926269297 33.72915930134169 chr18 78077248 84933463 1.0878132256915614 11.333712018238975 chr19 59128983 941696522 15.926141026305155 139.0238060973135 chr20 63025520 93552298 1.4843558291942693 14.246966809543977 chr21 48129895 29789662 0.6189430082903775 19.792023417768963 chr22 51304566 75220369 1.4661534998658794 17.326383087575724 chrMT 16571 2887987 174.2795848168487 89.76823150881008 chrX 155270560 41542985 0.26755223269626904 7.314368764417796 chrY 59373566 7288065 0.12274932248468956 7.842966732056475