BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008794.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,406,342 number of mapped reads = 1,161,035 (82.56%) number of supplementary alignments = 11,340 (0.81%) number of secondary alignments = 0 number of mapped bases = 75,820,298 bp number of sequenced bases = 75,786,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,703 duplication rate = 6.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1426 >>>>>>> ACTG content number of A's = 20,217,675 bp (26.68%) number of C's = 13,998,403 bp (18.47%) number of T's = 23,954,061 bp (31.61%) number of G's = 17,582,773 bp (23.2%) number of N's = 33,914 bp (0.04%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 638,368 number of insertions = 5,341 mapped reads with insertion percentage = 0.46% number of deletions = 19,511 mapped reads with deletion percentage = 1.66% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2741X There is a 1.74% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6654316 0.026697289552590524 0.4264099007977809 chr2 243199373 7604428 0.03126828785039672 0.335985375072076 chr3 198022430 5924320 0.02991741895097439 0.230446489354235 chr4 191154276 3261983 0.017064661425622518 0.1884419482304485 chr5 180915260 3775237 0.02086743263116666 0.1912341616155468 chr6 171115067 3401757 0.019879938451007356 0.19656987703302073 chr7 159138663 4307609 0.02706827441424464 0.30878333663711655 chr8 146364022 6394817 0.04369118115652766 0.4104763219895513 chr9 141213431 2149704 0.015223084552063606 0.22542186432067018 chr10 135534747 4174401 0.030799489373747088 0.2682286993918964 chr11 135006516 3363805 0.02491587146801122 0.3202231694924324 chr12 133851895 2657948 0.019857380427822854 0.18567798569768368 chr13 115169878 1929704 0.0167552838772652 0.170417751648656 chr14 107349540 2952495 0.027503564523890835 0.22429613166704027 chr15 102531392 2055861 0.020051039587953706 0.19036404830290335 chr16 90354753 1871016 0.020707444134123194 0.19819519167265234 chr17 81195210 2558666 0.03151252395307556 0.2725580774398795 chr18 78077248 1224654 0.015685158370336003 0.36260248111093146 chr19 59128983 1637776 0.02769836240883764 0.3091724370028438 chr20 63025520 1978576 0.03139325149558465 0.24043781919549093 chr21 48129895 885209 0.018392082509218022 0.18876747702216765 chr22 51304566 1208070 0.023547026983914063 0.20343086978950606 chrMT 16571 10505 0.6339388087622956 1.0672857827586575 chrX 155270560 3616540 0.023291859062014073 0.21975650527005022 chrY 59373566 220901 0.003720527751356555 0.1271640843427142