BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514744.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 15,320,948 number of mapped reads = 12,887,458 (84.12%) number of supplementary alignments = 2,411,071 (15.74%) number of secondary alignments = 0 number of mapped bases = 1,180,504,917 bp number of sequenced bases = 1,178,715,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,164,551 duplication rate = 41.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.5109 >>>>>>> ACTG content number of A's = 352,524,766 bp (29.91%) number of C's = 219,431,322 bp (18.62%) number of T's = 362,477,264 bp (30.75%) number of G's = 244,203,306 bp (20.72%) number of N's = 78,946 bp (0.01%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 9,891,791 number of insertions = 1,134,711 mapped reads with insertion percentage = 7.99% number of deletions = 563,065 mapped reads with deletion percentage = 4.06% homopolymer indels = 34.66% >>>>>>> Coverage mean coverageData = 0.3813X std coverageData = 61.0063X There is a 1.45% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 54354896 0.21807326209229386 10.408030108497764 chr2 243199373 126328862 0.5194456730774548 27.819843794101516 chr3 198022430 59771391 0.3018415186602851 12.461088719627126 chr4 191154276 85213068 0.4457816470712902 50.19843377282468 chr5 180915260 36241444 0.2003227588430075 8.757419078061396 chr6 171115067 65366934 0.3820057178249534 11.328025219605236 chr7 159138663 61625034 0.38724111940038103 24.706464372420033 chr8 146364022 52511500 0.3587732783128903 11.871954040710133 chr9 141213431 120951269 0.8565139175748799 180.0457888941607 chr10 135534747 27987979 0.20650039653669033 7.235401425221348 chr11 135006516 160057407 1.1855531995211253 184.11465670487513 chr12 133851895 43908964 0.32804140725837316 14.935560032719476 chr13 115169878 52311293 0.45420984990537194 11.619057573753539 chr14 107349540 27330848 0.2545967872801318 16.119132912781744 chr15 102531392 48325892 0.4713277666219532 104.07033198761971 chr16 90354753 17295013 0.1914123211647759 11.149251375671797 chr17 81195210 14309587 0.17623683712376628 35.23032205805095 chr18 78077248 28370187 0.36336048883280314 13.868939998178833 chr19 59128983 6375230 0.10781903690107439 5.342852430259561 chr20 63025520 17326244 0.2749083863171617 10.765852452944484 chr21 48129895 8389955 0.17431899654050773 5.694036569197415 chr22 51304566 7566404 0.14748012876670666 18.593846070237962 chrMT 16571 32387833 1954.488745398588 2069.00052903578 chrX 155270560 15175395 0.09773517272044359 4.5238810143000014 chrY 59373566 11022288 0.18564301830885482 6.289426150253588