BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008738.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 = 1,144,773 number of mapped reads = 864,400 (75.51%) number of supplementary alignments = 3,848 (0.34%) number of secondary alignments = 0 number of mapped bases = 57,023,114 bp number of sequenced bases = 56,995,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,107 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7546 >>>>>>> ACTG content number of A's = 16,352,599 bp (28.69%) number of C's = 10,200,250 bp (17.9%) number of T's = 17,128,884 bp (30.05%) number of G's = 13,310,732 bp (23.35%) number of N's = 3,116 bp (0.01%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 484,045 number of insertions = 4,614 mapped reads with insertion percentage = 0.53% number of deletions = 17,448 mapped reads with deletion percentage = 2% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.1832X There is a 1.72% 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 4938152 0.019811994771318946 0.24910694118326038 chr2 243199373 4911728 0.02019630206859127 0.23086065357751362 chr3 198022430 4779037 0.02413381655805355 0.16395262199479285 chr4 191154276 2869178 0.015009750553526723 0.13105780175728635 chr5 180915260 2691733 0.014878418769096648 0.127044892209178 chr6 171115067 2966090 0.017333891468481848 0.15363467119826618 chr7 159138663 3500208 0.021994705334429005 0.2480884274956592 chr8 146364022 4799264 0.032789916090171393 0.22831472470924047 chr9 141213431 1751065 0.01240013069295087 0.17376786428006474 chr10 135534747 3187830 0.023520389203220336 0.2100558472980405 chr11 135006516 2356706 0.01745623892701594 0.18397839283974202 chr12 133851895 2457748 0.018361697456730067 0.14321916832109005 chr13 115169878 1677201 0.014562844288156665 0.1261998307231356 chr14 107349540 2111164 0.019666260330505374 0.15065774577220206 chr15 102531392 1494759 0.01457854975771713 0.12724787460842615 chr16 90354753 1345259 0.01488863568693503 0.1368321697638561 chr17 81195210 1549988 0.01908964826866018 0.16441167994183173 chr18 78077248 834493 0.010688043205621181 0.27632949941432255 chr19 59128983 1061601 0.017953987133517924 0.17864543152130652 chr20 63025520 1244470 0.019745493571492946 0.1495887493624861 chr21 48129895 595667 0.012376237263762989 0.12146968937797976 chr22 51304566 705757 0.01375622200955759 0.1226259154932945 chrMT 16571 9424 0.5687043630438718 0.8608970213425157 chrX 155270560 3045012 0.01961100674847827 0.16196482193483586 chrY 59373566 139580 0.0023508778300430867 0.06416117878327911