BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234082.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 = 1,076,777 number of mapped reads = 618,317 (57.42%) number of supplementary alignments = 3,069 (0.29%) number of secondary alignments = 0 number of mapped bases = 39,575,843 bp number of sequenced bases = 39,552,170 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,347 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7857 >>>>>>> ACTG content number of A's = 11,144,898 bp (28.18%) number of C's = 6,564,111 bp (16.6%) number of T's = 12,892,179 bp (32.6%) number of G's = 8,941,177 bp (22.61%) number of N's = 9,805 bp (0.02%) GC percentage = 39.2% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 422,844 number of insertions = 3,465 mapped reads with insertion percentage = 0.55% number of deletions = 13,697 mapped reads with deletion percentage = 2.18% homopolymer indels = 45.8% >>>>>>> Coverage mean coverageData = 0.0128X std coverageData = 0.1661X There is a 1.17% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 3191837 0.01280573339073045 0.21805829781370736 chr2 243199373 3143918 0.012927327736161556 0.15820529705659353 chr3 198022430 3075263 0.01552987204530315 0.13525401445875565 chr4 191154276 2926638 0.01531034545102198 0.134455003151263 chr5 180915260 2661231 0.014709820498281902 0.1299712110389746 chr6 171115067 2215981 0.012950238917301186 0.13119183708242413 chr7 159138663 2321356 0.014587002028539098 0.18624342963069035 chr8 146364022 1892480 0.012929953510023112 0.3886454825075056 chr9 141213431 1444572 0.010229706832914498 0.13057751646578236 chr10 135534747 1880368 0.01387369690519288 0.1418050169969692 chr11 135006516 1702546 0.012610843168488253 0.139850234142756 chr12 133851895 1931407 0.01442943336737967 0.12919832877912665 chr13 115169878 1441937 0.012520087934798368 0.12140290208586076 chr14 107349540 1348853 0.012565056170711119 0.12413015661144108 chr15 102531392 931057 0.009080701840076451 0.10359767504346847 chr16 90354753 902474 0.009988118721325042 0.1104146906481736 chr17 81195210 919332 0.011322490575490845 0.11700785643116142 chr18 78077248 1150774 0.014738916002777148 0.22926897848429026 chr19 59128983 752395 0.012724639623854176 0.1526115333241901 chr20 63025520 808553 0.012828977848972923 0.12472465255628637 chr21 48129895 574980 0.011946421241932898 0.11907494075580821 chr22 51304566 363526 0.007085646139175995 0.08974457196520699 chrMT 16571 15259 0.9208255385915153 1.2278512137671513 chrX 155270560 1870201 0.012044788142710375 0.1208865874164597 chrY 59373566 108905 0.001834233773325995 0.05217210889574383