BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514745.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 = 117,615,784 number of mapped reads = 116,756,541 (99.27%) number of supplementary alignments = 10,142,707 (8.62%) number of secondary alignments = 0 number of mapped bases = 11,085,510,204 bp number of sequenced bases = 11,071,649,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,602,141 duplication rate = 51.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.6683 >>>>>>> ACTG content number of A's = 3,115,596,797 bp (28.14%) number of C's = 2,394,462,526 bp (21.63%) number of T's = 3,132,391,014 bp (28.29%) number of G's = 2,425,610,116 bp (21.91%) number of N's = 3,589,175 bp (0.03%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 89,553,387 number of insertions = 5,933,839 mapped reads with insertion percentage = 4.9% number of deletions = 5,214,654 mapped reads with deletion percentage = 4.24% homopolymer indels = 35.21% >>>>>>> Coverage mean coverageData = 3.5809X std coverageData = 672.4837X There is a 4.15% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.84% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.46% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.38% of reference with a coverageData >= 15X There is a 0.37% of reference with a coverageData >= 16X There is a 0.36% of reference with a coverageData >= 17X There is a 0.35% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.34% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.32% of reference with a coverageData >= 22X There is a 0.32% of reference with a coverageData >= 23X There is a 0.31% of reference with a coverageData >= 24X There is a 0.31% of reference with a coverageData >= 25X There is a 0.3% of reference with a coverageData >= 26X There is a 0.3% of reference with a coverageData >= 27X There is a 0.29% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.28% of reference with a coverageData >= 33X There is a 0.27% of reference with a coverageData >= 34X There is a 0.27% of reference with a coverageData >= 35X There is a 0.27% of reference with a coverageData >= 36X There is a 0.26% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.26% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.25% of reference with a coverageData >= 42X There is a 0.25% of reference with a coverageData >= 43X There is a 0.25% of reference with a coverageData >= 44X There is a 0.25% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.24% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.24% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 726237662 2.9136844637991897 314.47282776735733 chr2 243199373 785881018 3.2314269905621837 203.32048261118643 chr3 198022430 653087658 3.298048902843986 180.79138608500259 chr4 191154276 693050550 3.6256084064789635 238.79287680169236 chr5 180915260 600822238 3.321014700473581 175.6120293019123 chr6 171115067 630549250 3.684942892842978 296.37338693631995 chr7 159138663 551036794 3.462620482113765 224.4504023962389 chr8 146364022 363833276 2.485810864093363 119.596291038543 chr9 141213431 1519735704 10.76197705301842 2903.6502225704257 chr10 135534747 645008269 4.758988254133827 561.6682290081694 chr11 135006516 404468714 2.995919945078799 163.1235967655563 chr12 133851895 465123265 3.4749098247731194 216.53031982284483 chr13 115169878 420296994 3.649365626661513 519.7394129593794 chr14 107349540 249621393 2.3253140441961837 136.6520910796318 chr15 102531392 306778527 2.9920448851411283 222.06756848216222 chr16 90354753 224010322 2.479231192187532 98.72267283877109 chr17 81195210 247860886 3.052654042030312 186.80991558112748 chr18 78077248 445750862 5.709100582028711 284.900749266931 chr19 59128983 84206335 1.424112689372655 69.95313201509023 chr20 63025520 364077490 5.776667768865691 532.6963138798861 chr21 48129895 126993644 2.638560586928353 213.8634337085622 chr22 51304566 144295033 2.8125183438838564 125.97737031009935 chrMT 16571 2287104 138.0184659948102 301.13268725168325 chrX 155270560 229074657 1.4753257604017143 134.97970890048688 chrY 59373566 201422559 3.3924618743634163 169.63212982020826