BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714115.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 = 585,478 number of mapped reads = 520,072 (88.83%) number of supplementary alignments = 13,011 (2.22%) number of secondary alignments = 0 number of mapped bases = 68,349,874 bp number of sequenced bases = 66,630,649 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 466,435 duplication rate = 44.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6046 >>>>>>> ACTG content number of A's = 17,595,070 bp (26.41%) number of C's = 15,200,931 bp (22.81%) number of T's = 16,761,644 bp (25.16%) number of G's = 17,072,485 bp (25.62%) number of N's = 519 bp (0%) GC percentage = 48.44% >>>>>>> Mismatches and indels general error rate = 0.0458 number of mismatches = 2,898,138 number of insertions = 65,417 mapped reads with insertion percentage = 12.14% number of deletions = 270,740 mapped reads with deletion percentage = 49.44% homopolymer indels = 28.43% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 7.233X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 0.01% 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 6851019 0.027486467124990633 7.233852113100677 chr2 243199373 6672323 0.027435609383746232 7.944225871570587 chr3 198022430 1992302 0.010060991575550305 1.6677513034267362 chr4 191154276 2215468 0.01158994737842014 2.7147375086923295 chr5 180915260 3203958 0.017709716692776496 3.7335974433290757 chr6 171115067 2356047 0.013768787525881634 2.4310893254075885 chr7 159138663 1812390 0.011388747183329044 1.973832196467974 chr8 146364022 2155609 0.014727724549684757 2.584936818441768 chr9 141213431 2930417 0.02075168756433657 5.445013005415933 chr10 135534747 2912022 0.021485427644617215 3.4089309584116014 chr11 135006516 3493224 0.02587448445821682 4.613399698745024 chr12 133851895 4118798 0.03077130884101417 7.413814039808989 chr13 115169878 2111647 0.01833506327062359 6.4506676983472095 chr14 107349540 5578512 0.05196586776245152 29.05039090360992 chr15 102531392 2594080 0.025300348989702588 4.548441514054971 chr16 90354753 1498752 0.016587417376925373 2.3323367831596866 chr17 81195210 2573759 0.03169840930271626 6.383945161748253 chr18 78077248 1901858 0.02435867104332366 5.809962727803024 chr19 59128983 2282715 0.0386056868253594 4.511430560375592 chr20 63025520 2133534 0.03385190633889256 6.915337629839919 chr21 48129895 621051 0.012903643359288442 2.3626713673557616 chr22 51304566 554707 0.010812039614563741 1.177402887753605 chrMT 16571 47131 2.8441856254903146 20.400521181567793 chrX 155270560 5381011 0.0346557067869144 3.498617235249814 chrY 59373566 357540 0.0060218717535005396 1.0945756359877619