BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013324.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 = 1,953,849 number of mapped reads = 1,637,719 (83.82%) number of supplementary alignments = 20,484 (1.05%) number of secondary alignments = 0 number of mapped bases = 108,052,030 bp number of sequenced bases = 108,003,016 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 268,044 duplication rate = 11.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2915 >>>>>>> ACTG content number of A's = 29,330,666 bp (27.16%) number of C's = 20,782,478 bp (19.24%) number of T's = 33,316,131 bp (30.85%) number of G's = 24,559,921 bp (22.74%) number of N's = 13,820 bp (0.01%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 849,368 number of insertions = 8,056 mapped reads with insertion percentage = 0.49% number of deletions = 28,690 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.08% >>>>>>> Coverage mean coverageData = 0.0349X std coverageData = 0.4853X There is a 1.53% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 2227911 0.008938437108246964 0.585638454987189 chr2 243199373 2401027 0.009872669367449398 0.6079341339199379 chr3 198022430 3064563 0.015475837762419136 0.22493836888729585 chr4 191154276 2960352 0.01548671608057567 0.2372182334560616 chr5 180915260 17192107 0.09502850671634885 0.6201384630736279 chr6 171115067 6172812 0.03607404133500412 0.40450662087184 chr7 159138663 2640205 0.016590594329675874 0.29798984976281295 chr8 146364022 7691996 0.05255387146986163 0.6535841672036947 chr9 141213431 1155849 0.008185120861485195 0.33756881249767046 chr10 135534747 11290968 0.0833068143034937 0.7163875256153394 chr11 135006516 9246248 0.06848742026644107 0.6645860248328442 chr12 133851895 4976055 0.03717582780579984 0.38165944039073435 chr13 115169878 680378 0.005907603722563637 0.13784656008774374 chr14 107349540 1025322 0.009551247261981746 0.17195406728867949 chr15 102531392 4479000 0.043684182108831605 0.41019932517689706 chr16 90354753 1482390 0.01640633116444909 0.2529436998203042 chr17 81195210 6844496 0.08429679534051332 0.6240344340383078 chr18 78077248 11508509 0.14739900924786695 0.9292289495277198 chr19 59128983 1099713 0.018598544135284723 0.5911522392711115 chr20 63025520 5612475 0.08905083210737491 0.5996607971016135 chr21 48129895 965502 0.020060338797747223 0.2674371262428345 chr22 51304566 1080184 0.021054344363813544 0.2729086888992932 chrMT 16571 7871 0.4749864220626395 0.9841613279489139 chrX 155270560 2028270 0.013062811134319346 0.2701593716768661 chrY 59373566 217827 0.003668753869356609 0.12952890900116334