BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714121.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 654,230 number of mapped reads = 481,397 (73.58%) number of supplementary alignments = 13,118 (2.01%) number of secondary alignments = 0 number of mapped bases = 62,707,261 bp number of sequenced bases = 61,243,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 421,205 duplication rate = 43.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6628 >>>>>>> ACTG content number of A's = 16,750,184 bp (27.35%) number of C's = 12,474,604 bp (20.37%) number of T's = 15,942,097 bp (26.03%) number of G's = 16,075,787 bp (26.25%) number of N's = 508 bp (0%) GC percentage = 46.62% >>>>>>> Mismatches and indels general error rate = 0.0466 number of mismatches = 2,655,609 number of insertions = 74,928 mapped reads with insertion percentage = 14.83% number of deletions = 233,396 mapped reads with deletion percentage = 45.04% homopolymer indels = 29.63% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 5.381X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4505514 0.018076239818074515 2.979249403394406 chr2 243199373 8187365 0.033665238931352016 14.767025434021265 chr3 198022430 2702972 0.013649827446315045 2.512755313575465 chr4 191154276 2505507 0.013107250606311313 2.0299250472742103 chr5 180915260 4000399 0.022112004261000427 3.9480350324443485 chr6 171115067 2226715 0.013012968635894582 2.2697818323068653 chr7 159138663 3689353 0.023183259997603473 4.661246710497513 chr8 146364022 2713307 0.018538073516454746 3.805331027008075 chr9 141213431 2777449 0.019668447826326096 3.6015038330675733 chr10 135534747 3349327 0.024711943425105593 5.037150282426928 chr11 135006516 3455382 0.02559418687613567 7.054677490320957 chr12 133851895 2607279 0.019478835170768406 2.6894191770650373 chr13 115169878 1672200 0.01451942147581332 2.2653694726667557 chr14 107349540 2393059 0.022292214759373912 4.255432458916831 chr15 102531392 1598115 0.015586592250693329 1.9884403069480556 chr16 90354753 1091671 0.012082053945739855 1.4900194064800878 chr17 81195210 1488547 0.018332941068814283 2.635011288047466 chr18 78077248 1322097 0.016933191600195744 1.9407028165754445 chr19 59128983 1107247 0.018725960498931632 2.529168943973987 chr20 63025520 1172040 0.018596276555909414 2.895370188083829 chr21 48129895 578306 0.012015525901313518 2.3634709772812 chr22 51304566 1273719 0.02482662069492996 6.382744077750668 chrMT 16571 375133 22.637921670388028 180.83081075893782 chrX 155270560 5648153 0.03637620035633284 3.8056792305410405 chrY 59373566 266405 0.004486929419061675 0.9313179180108375