BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524825.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,480,100 number of mapped reads = 1,344,832 (90.86%) number of supplementary alignments = 4,347 (0.29%) number of secondary alignments = 0 number of mapped bases = 76,666,373 bp number of sequenced bases = 76,642,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,130 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6116 >>>>>>> ACTG content number of A's = 18,316,857 bp (23.9%) number of C's = 14,826,447 bp (19.34%) number of T's = 24,099,056 bp (31.44%) number of G's = 19,391,683 bp (25.3%) number of N's = 8,425 bp (0.01%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 386,514 number of insertions = 6,036 mapped reads with insertion percentage = 0.45% number of deletions = 14,778 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.2203X There is a 2.22% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6129233 0.02459064284537931 0.23687331112866986 chr2 243199373 6370870 0.026196079049924194 0.36133273393500437 chr3 198022430 4987006 0.025184046069932582 0.17508469303892235 chr4 191154276 4892274 0.025593327559149136 0.20492348211399078 chr5 180915260 4562240 0.025217552129101768 0.17340288043274069 chr6 171115067 4337659 0.02534936914701965 0.19074972096650622 chr7 159138663 4192946 0.026347751834511768 0.2549439313473846 chr8 146364022 3794981 0.025928373299279793 0.19834439265986584 chr9 141213431 3272591 0.023174785690179854 0.19317326454737585 chr10 135534747 3769713 0.027813627748167043 0.28317098861976886 chr11 135006516 3490156 0.02585175962914264 0.20260681742793815 chr12 133851895 3437167 0.0256788818716388 0.1774922661558022 chr13 115169878 2346322 0.020372705439524734 0.15680669965694943 chr14 107349540 2320707 0.02161822957042946 0.16327147853782303 chr15 102531392 2202937 0.021485488073740382 0.16323094818960493 chr16 90354753 2401404 0.02657750611082961 0.19736234864383648 chr17 81195210 2225801 0.027412959459061685 0.19032251316446427 chr18 78077248 1992462 0.025519111534258995 0.29698900929367256 chr19 59128983 1738748 0.029406019041457215 0.23339516188347775 chr20 63025520 1689006 0.026798763421547335 0.19149378095765043 chr21 48129895 1017290 0.021136343638397715 0.1753375001505134 chr22 51304566 1003289 0.019555549890042927 0.15441589539900552 chrMT 16571 11587 0.699233600868988 1.037332783846858 chrX 155270560 4213820 0.027138563807588507 0.19174174390219337 chrY 59373566 266164 0.004482870373660898 0.13023253847701183