BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237327.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 = 3,211,933 number of mapped reads = 2,761,559 (85.98%) number of supplementary alignments = 30,027 (0.93%) number of secondary alignments = 0 number of mapped bases = 167,844,022 bp number of sequenced bases = 167,761,931 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,066,840 duplication rate = 22.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4517 >>>>>>> ACTG content number of A's = 42,716,534 bp (25.46%) number of C's = 29,763,419 bp (17.74%) number of T's = 55,131,625 bp (32.86%) number of G's = 40,133,038 bp (23.92%) number of N's = 17,315 bp (0.01%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,086,011 number of insertions = 12,310 mapped reads with insertion percentage = 0.44% number of deletions = 47,877 mapped reads with deletion percentage = 1.72% homopolymer indels = 43.73% >>>>>>> Coverage mean coverageData = 0.0542X std coverageData = 0.7917X There is a 1.65% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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% 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 12974527 0.052054141120876085 0.6844571426988374 chr2 243199373 14769476 0.06072990985877254 1.4802571491887304 chr3 198022430 10967298 0.05538411986965315 0.5952740383505793 chr4 191154276 7631208 0.039921722703184524 0.5850698443258292 chr5 180915260 8479206 0.046868384679103356 0.5627453063167063 chr6 171115067 12975335 0.07582812681246824 0.8535217057615759 chr7 159138663 9881531 0.062093842022538544 0.8201796147409088 chr8 146364022 13068870 0.08929018088885259 0.9289402026769412 chr9 141213431 7532598 0.05334193742520143 0.6441366958543158 chr10 135534747 5838136 0.04307482862678749 0.7476976084619574 chr11 135006516 4427026 0.0327912024631463 0.5372652964911306 chr12 133851895 6287289 0.04697198347472033 0.570979083480024 chr13 115169878 5590922 0.048545002365983234 0.641839359911015 chr14 107349540 6256402 0.0582806596097198 0.6057301492783111 chr15 102531392 4785725 0.046675704939224856 0.5661749812377168 chr16 90354753 3454725 0.038235121953130675 0.5158737502325841 chr17 81195210 3790945 0.04668926898520245 0.5786000668293219 chr18 78077248 4877389 0.06246876170635522 1.4840193671555932 chr19 59128983 1255638 0.02123557579199358 0.4956918507266593 chr20 63025520 5550001 0.0880595828483446 0.7534851258945794 chr21 48129895 3414495 0.07094332950445871 0.7011660198174152 chr22 51304566 2009082 0.03915990635219485 0.5098953889842796 chrMT 16571 23666 1.4281576247661578 3.3432124789033457 chrX 155270560 11354844 0.07312940714582339 0.7337624988684087 chrY 59373566 647688 0.010908692935842863 0.37261100976936223