BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971291.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,796,278 number of mapped reads = 5,743,273 (84.51%) number of secondary alignments = 0 number of mapped bases = 226,688,977 bp number of sequenced bases = 226,665,535 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 274,902 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0881 >>>>>>> ACTG content number of A's = 66,916,501 bp (29.52%) number of C's = 45,461,858 bp (20.06%) number of T's = 67,976,343 bp (29.99%) number of G's = 46,299,040 bp (20.43%) number of N's = 11,793 bp (0.01%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 660,524 number of insertions = 7,617 mapped reads with insertion percentage = 0.13% number of deletions = 18,799 mapped reads with deletion percentage = 0.33% homopolymer indels = 40.79% >>>>>>> Coverage mean coverageData = 0.0732X std coverageData = 0.6826X There is a 6.16% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 17898558 0.07180948207146091 1.235167002133542 chr2 243199373 19506917 0.08020956945476994 0.5181226695265184 chr3 198022430 15348777 0.07751029517211762 0.3197643644342806 chr4 191154276 15754723 0.0824188887095573 0.3496494452689201 chr5 180915260 14437984 0.07980523036033556 0.33039838711685227 chr6 171115067 13817273 0.08074842994392774 0.4251135759669504 chr7 159138663 12829020 0.0806153561815459 0.9562327443471603 chr8 146364022 11384161 0.07777977705477375 1.6352001621575245 chr9 141213431 9439216 0.06684361348036363 0.5023462746747065 chr10 135534747 10463878 0.0772043939403967 0.5641881249939417 chr11 135006516 10373966 0.07684048375857651 0.434882282978725 chr12 133851895 10385822 0.07759189363736688 0.3315621810232242 chr13 115169878 7185485 0.06239031528712742 0.2813020107339642 chr14 107349540 7062179 0.06578676536480733 0.37262532896170825 chr15 102531392 6195391 0.06042433326175851 0.2794149344401273 chr16 90354753 5811728 0.0643212206003153 0.35021823865632334 chr17 81195210 5386399 0.06633887639430947 0.31445249925325286 chr18 78077248 6094693 0.0780597825374173 0.9463426163577071 chr19 59128983 3822567 0.06464794092602608 1.166176141356582 chr20 63025520 4353020 0.06906757770503123 0.3231378753781336 chr21 48129895 2875275 0.05973989762495846 0.3298453012781139 chr22 51304566 2171733 0.042330208972043544 0.23460152100307496 chrMT 16571 11562 0.6977249411622715 0.981566114582646 chrX 155270560 13313869 0.08574625479550019 0.4217858922049866 chrY 59373566 764781 0.01288083319772304 0.19741943221022776