BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068954.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 = 2,061,288 number of mapped reads = 1,538,613 (74.64%) number of supplementary alignments = 12,350 (0.6%) number of secondary alignments = 0 number of mapped bases = 102,189,404 bp number of sequenced bases = 102,144,019 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,780 duplication rate = 5.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8603 >>>>>>> ACTG content number of A's = 28,161,770 bp (27.57%) number of C's = 17,943,372 bp (17.57%) number of T's = 33,739,571 bp (33.03%) number of G's = 22,049,595 bp (21.59%) number of N's = 249,711 bp (0.24%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,045,815 number of insertions = 8,690 mapped reads with insertion percentage = 0.56% number of deletions = 27,684 mapped reads with deletion percentage = 1.78% homopolymer indels = 48.73% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.2847X There is a 2.48% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.15% 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 11743717 0.04711609926139362 0.33461594390730515 chr2 243199373 10073973 0.041422693141564965 0.34906093677311745 chr3 198022430 14794365 0.07471055172891274 0.3473592553403989 chr4 191154276 8268519 0.04325573653398159 0.2667132263648327 chr5 180915260 5170248 0.028578285767601914 0.21486228857344053 chr6 171115067 15495923 0.09055849535447395 0.4164072807640886 chr7 159138663 5228653 0.03285595656914624 0.24315934872206824 chr8 146364022 2816452 0.01924278905098686 0.3672343950700125 chr9 141213431 2489434 0.017628875542298805 0.1826394050049223 chr10 135534747 1747526 0.012893564482029099 0.1582233798369611 chr11 135006516 5934110 0.04395424884529277 0.4661698114413528 chr12 133851895 1910961 0.014276682448164069 0.15317052754329075 chr13 115169878 553995 0.004810242136403062 0.08563499441988164 chr14 107349540 871047 0.008114119538844786 0.11951996710511727 chr15 102531392 1143705 0.011154681290194519 0.1332525797146445 chr16 90354753 1104105 0.012219667071637061 0.14010859774148726 chr17 81195210 1159655 0.014282308032702914 0.2043946258974689 chr18 78077248 1026133 0.013142535454118465 0.32556536572343137 chr19 59128983 860263 0.014548922649320723 0.24016947910302272 chr20 63025520 677400 0.010748027148367836 0.1455379322361707 chr21 48129895 1121095 0.023293111277304886 0.19438396631864718 chr22 51304566 242245 0.004721704497022741 0.0838268168780123 chrMT 16571 318916 19.24542876108865 10.132630267223021 chrX 155270560 7248325 0.04668190157876677 0.298159167412083 chrY 59373566 188639 0.0031771546280376694 0.07090167059313383