BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524774.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 = 1,429,042 number of mapped reads = 1,314,900 (92.01%) number of supplementary alignments = 5,169 (0.36%) number of secondary alignments = 0 number of mapped bases = 76,024,727 bp number of sequenced bases = 76,000,848 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,758 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6961 >>>>>>> ACTG content number of A's = 17,777,226 bp (23.39%) number of C's = 14,261,092 bp (18.76%) number of T's = 24,389,065 bp (32.09%) number of G's = 19,564,171 bp (25.74%) number of N's = 9,294 bp (0.01%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 379,230 number of insertions = 4,530 mapped reads with insertion percentage = 0.34% number of deletions = 14,702 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.13% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2238X There is a 2.21% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 6091156 0.024437876927095 0.30511228245792665 chr2 243199373 6353066 0.026122871624344197 0.34953703432844757 chr3 198022430 5004514 0.025272460296543175 0.1745722059726275 chr4 191154276 4869360 0.02547345579651067 0.19723033405063872 chr5 180915260 4521148 0.024990418165941337 0.17188164122354346 chr6 171115067 4263570 0.02491639149461923 0.1833437880190654 chr7 159138663 4170408 0.026206126917127613 0.25529058581246394 chr8 146364022 3792529 0.02591162054838859 0.20547401222242498 chr9 141213431 3243220 0.02296679555926943 0.19259779524813947 chr10 135534747 3740801 0.027600309756729762 0.2680246862647897 chr11 135006516 3409162 0.025251833030044267 0.19618779519926577 chr12 133851895 3419163 0.02554437499745521 0.17605070085106964 chr13 115169878 2321675 0.020158699829481454 0.15358452800088332 chr14 107349540 2280789 0.021246378885275148 0.16366563633434883 chr15 102531392 2213764 0.021591085001557375 0.16041626532777364 chr16 90354753 2330785 0.025795931288750244 0.19272558024664802 chr17 81195210 2201131 0.027109123801761212 0.1867451851425824 chr18 78077248 1968426 0.02521126256909055 0.2985706682673684 chr19 59128983 1715044 0.029005132728225684 0.2575406276252712 chr20 63025520 1650587 0.026189184952381196 0.18336478813441343 chr21 48129895 1011090 0.021007525572204137 0.17449857902252736 chr22 51304566 951386 0.01854388554812061 0.149981354500779 chrMT 16571 42743 2.5793856737674252 2.137325062605676 chrX 155270560 4206952 0.02709433134008147 0.19029622364357116 chrY 59373566 252258 0.004248658401282484 0.12030439236504568