BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231838.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 = 11,580,835 number of mapped reads = 4,620,700 (39.9%) number of supplementary alignments = 36,961 (0.32%) number of secondary alignments = 0 number of mapped bases = 301,710,834 bp number of sequenced bases = 301,603,456 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 320,007 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0411 >>>>>>> ACTG content number of A's = 85,540,987 bp (28.36%) number of C's = 61,121,162 bp (20.27%) number of T's = 80,012,380 bp (26.53%) number of G's = 74,905,937 bp (24.84%) number of N's = 22,990 bp (0.01%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,034,075 number of insertions = 25,480 mapped reads with insertion percentage = 0.54% number of deletions = 63,232 mapped reads with deletion percentage = 1.35% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 0.0975X std coverageData = 17.9616X There is a 7.85% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 34650934 0.139020452029285 2.5300157388923044 chr2 243199373 34149878 0.14041926826842602 63.97516604339354 chr3 198022430 22250522 0.11236364486588717 0.4106061015829019 chr4 191154276 9729741 0.05089993906283321 0.35642220860363877 chr5 180915260 10191496 0.05633298152958462 0.2950533866884126 chr6 171115067 19819915 0.11582799427007792 0.6761542877367496 chr7 159138663 18132245 0.11393991037866141 1.5524727344834832 chr8 146364022 18234158 0.12458087548318397 0.8544025230047035 chr9 141213431 15588537 0.11038990335133207 0.9335343988985982 chr10 135534747 16215496 0.11964087703649899 1.1762832426310839 chr11 135006516 9074153 0.06721270401496769 0.7648078729661134 chr12 133851895 10933633 0.08168455889249832 0.35566416019928987 chr13 115169878 6928550 0.06015939341361463 0.2710927880288246 chr14 107349540 13166628 0.12265192752572578 0.6768631254431258 chr15 102531392 4290458 0.0418453111413917 0.2330683855403583 chr16 90354753 8855200 0.09800480556899978 0.6193638533890627 chr17 81195210 8527742 0.1050276487984944 0.531424684078437 chr18 78077248 6430874 0.08236553112117886 2.1752344341325855 chr19 59128983 6794229 0.1149052233825838 1.595197832800632 chr20 63025520 8179385 0.12977893716703964 0.45428473079395376 chr21 48129895 5592289 0.11619158944768111 0.48358383602195965 chr22 51304566 3251119 0.06336899916471372 0.2863803187563501 chrMT 16571 238801 14.410777864944784 7.7801111186573255 chrX 155270560 9744886 0.06276068045352577 0.4201151738064053 chrY 59373566 739965 0.012462869419027316 0.2766510738159412