BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927012.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 23,054,690 number of mapped reads = 22,181,953 (96.21%) number of supplementary alignments = 811,660 (3.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,069,403 number of mapped paired reads (second in pair) = 11,112,550 number of mapped paired reads (both in pair) = 21,613,550 number of mapped paired reads (singletons) = 568,403 number of mapped bases = 2,011,270,148 bp number of sequenced bases = 2,009,707,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,961,798 duplication rate = 7.06% >>>>>>> Insert size mean insert size = 426,819.0521 std insert size = 6,345,085.4837 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 52.6313 >>>>>>> ACTG content number of A's = 583,948,567 bp (29.06%) number of C's = 375,691,585 bp (18.69%) number of T's = 599,001,000 bp (29.81%) number of G's = 450,709,753 bp (22.43%) number of N's = 356,402 bp (0.02%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 20,599,214 number of insertions = 352,732 mapped reads with insertion percentage = 1.56% number of deletions = 1,096,063 mapped reads with deletion percentage = 4.81% homopolymer indels = 52.65% >>>>>>> Coverage mean coverageData = 0.6497X std coverageData = 2.3312X There is a 30.02% of reference with a coverageData >= 1X There is a 14.88% of reference with a coverageData >= 2X There is a 7.86% of reference with a coverageData >= 3X There is a 4.41% of reference with a coverageData >= 4X There is a 2.58% of reference with a coverageData >= 5X There is a 1.55% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% 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 0.03% 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 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 160383976 0.6434646997328846 2.7751519389733574 chr2 243199373 177567903 0.7301330624729859 3.7364165917249688 chr3 198022430 135148591 0.6824913268663555 1.4292813907598358 chr4 191154276 128601026 0.6727603938088207 1.8994721362455138 chr5 180915260 125577146 0.6941213582535823 1.4141977985994405 chr6 171115067 119271501 0.6970251252041996 1.8984180997125886 chr7 159138663 106592543 0.6698092153759014 1.9879454259087612 chr8 146364022 103671058 0.7083097101554097 1.6375724804839429 chr9 141213431 84117273 0.595674734367158 2.9332094035993586 chr10 135534747 98835214 0.7292241745210917 4.657685832959642 chr11 135006516 94405933 0.6992694560016643 2.062100892490389 chr12 133851895 89024680 0.6650983910239 1.4203746925264737 chr13 115169878 64279843 0.5581306858725682 1.2800275267825247 chr14 107349540 62193527 0.5793553190819448 1.3740781823350798 chr15 102531392 58176940 0.5674061267011765 1.3505695806324254 chr16 90354753 58976660 0.6527233824655577 2.8942754203869105 chr17 81195210 46760980 0.5759081108356022 1.5710028863106307 chr18 78077248 55400335 0.7095579880069544 2.8422159687064377 chr19 59128983 28027771 0.47401070639080667 1.892931137115036 chr20 63025520 44958205 0.7133333449688317 1.540651693161408 chr21 48129895 25762799 0.5352764430506237 1.8449442919092303 chr22 51304566 21976698 0.42835754618799426 1.1871660364484407 chrMT 16571 111942 6.755295395570575 7.609198325607052 chrX 155270560 118222972 0.761399791435028 1.646767694209453 chrY 59373566 3224632 0.05431090327301547 1.8031828077223873