BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081939.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,704,821 number of mapped reads = 2,471,470 (91.37%) number of supplementary alignments = 15,287 (0.57%) number of secondary alignments = 0 number of mapped bases = 167,919,328 bp number of sequenced bases = 167,857,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,131 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7783 >>>>>>> ACTG content number of A's = 47,171,935 bp (28.1%) number of C's = 31,131,942 bp (18.55%) number of T's = 52,493,886 bp (31.27%) number of G's = 37,038,591 bp (22.07%) number of N's = 21,414 bp (0.01%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,339,780 number of insertions = 12,799 mapped reads with insertion percentage = 0.51% number of deletions = 34,824 mapped reads with deletion percentage = 1.39% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.0542X std coverageData = 0.6104X There is a 4.64% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 15807129 0.06341861431109534 1.1496774934906566 chr2 243199373 15063584 0.06193923863446803 0.8795120240243189 chr3 198022430 9772104 0.04934847027177679 0.25400682481178344 chr4 191154276 8906231 0.04659184814678171 0.28127329749700236 chr5 180915260 8617119 0.04763069184987491 0.249696324044719 chr6 171115067 14879820 0.08695797664620615 0.4817274280434604 chr7 159138663 11449800 0.07194857480988137 0.9192226973510932 chr8 146364022 9929223 0.06783923305961079 0.6835682564886552 chr9 141213431 7985348 0.056548077215119855 0.6814200051797447 chr10 135534747 7095209 0.05234974172342684 0.6157993062041917 chr11 135006516 6046590 0.0447873938173473 0.3972278766834456 chr12 133851895 7366198 0.0550324520993894 0.28263516984008596 chr13 115169878 4624981 0.040157904829941735 0.22241428320110107 chr14 107349540 4374884 0.04075363527407756 0.28890044515839863 chr15 102531392 3723494 0.03631564857716942 0.22350831979621436 chr16 90354753 3799266 0.04204832478486217 0.30300671607903223 chr17 81195210 4588438 0.05651119074635068 0.3297062020158348 chr18 78077248 4929342 0.06313416681899443 1.079666107536647 chr19 59128983 3573043 0.06042794613937466 0.872778664400098 chr20 63025520 4299296 0.06821516109664784 0.3110180013340805 chr21 48129895 1848531 0.038407127212722984 0.26647365669678175 chr22 51304566 1394141 0.027173819187945182 0.18137881465425587 chrMT 16571 96108 5.799770683724579 3.6374319817066207 chrX 155270560 7355760 0.04737382282900249 0.336450491601677 chrY 59373566 393689 0.006630711721104978 0.19168010283178966