BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238652.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 = 3,618,867 number of mapped reads = 3,231,946 (89.31%) number of supplementary alignments = 31,398 (0.87%) number of secondary alignments = 0 number of mapped bases = 198,970,356 bp number of sequenced bases = 198,880,338 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 953,970 duplication rate = 20.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.6701 >>>>>>> ACTG content number of A's = 50,108,117 bp (25.2%) number of C's = 34,506,150 bp (17.35%) number of T's = 67,330,548 bp (33.85%) number of G's = 46,931,088 bp (23.6%) number of N's = 4,435 bp (0%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,122,945 number of insertions = 12,998 mapped reads with insertion percentage = 0.4% number of deletions = 52,414 mapped reads with deletion percentage = 1.61% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 0.0643X std coverageData = 1.0692X There is a 2.88% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% 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 6395285 0.025658050416652724 0.8000003641245979 chr2 243199373 7573876 0.03114266252651893 2.039640483296669 chr3 198022430 7044351 0.03557350043628896 0.3710516121198898 chr4 191154276 6490454 0.03395400895975772 0.3669520257919564 chr5 180915260 5689607 0.031449016517456845 0.3463024604238204 chr6 171115067 20908447 0.12218939785121319 1.020365970908214 chr7 159138663 34960240 0.21968413797720546 2.8904985577528963 chr8 146364022 12372173 0.08453015181558758 0.777285258894397 chr9 141213431 6428320 0.04552201553689323 0.5404666669571304 chr10 135534747 4704578 0.034711231651909896 0.5943002504275386 chr11 135006516 9063689 0.06713519664487898 0.5316175507670969 chr12 133851895 4128758 0.03084571944237323 0.35976509640024634 chr13 115169878 11476842 0.09965142100784373 0.7089457534839267 chr14 107349540 886295 0.008256160203387923 0.24646092831298053 chr15 102531392 6817356 0.06649042665879344 0.6001359901888259 chr16 90354753 10224769 0.11316249185031804 0.7048121697884174 chr17 81195210 2945222 0.036273346666632185 0.36424154474916837 chr18 78077248 11332831 0.14514895555744997 1.754617608763889 chr19 59128983 1948198 0.03294827512930503 0.6505318739721453 chr20 63025520 4085610 0.06482469323537512 0.50162559628472 chr21 48129895 753373 0.01565291177136372 0.28730731946996807 chr22 51304566 310678 0.006055562384057591 0.1196959822166944 chrMT 16571 34293 2.0694586928972303 3.2555693184841163 chrX 155270560 21773976 0.1402324819334715 0.7721408119914477 chrY 59373566 621135 0.010461473713739882 0.3587356850904337