BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524375.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 = 1,469,961 number of mapped reads = 1,356,085 (92.25%) number of supplementary alignments = 4,902 (0.33%) number of secondary alignments = 0 number of mapped bases = 79,268,760 bp number of sequenced bases = 79,245,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,206 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7585 >>>>>>> ACTG content number of A's = 19,771,532 bp (24.95%) number of C's = 16,070,497 bp (20.28%) number of T's = 25,342,882 bp (31.98%) number of G's = 18,050,287 bp (22.78%) number of N's = 10,561 bp (0.01%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 385,734 number of insertions = 6,183 mapped reads with insertion percentage = 0.45% number of deletions = 14,655 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 0.0256X std coverageData = 0.2561X There is a 2.33% of reference with a coverageData >= 1X There is a 0.17% 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 6368860 0.025552032626630847 0.48313985313107344 chr2 243199373 6652124 0.027352554070935044 0.2858709067876498 chr3 198022430 5273134 0.026628973293580934 0.17517454426313528 chr4 191154276 5166367 0.02702721125631529 0.19216141271264997 chr5 180915260 4872509 0.026932548420735763 0.1769632401788952 chr6 171115067 4504966 0.026327114724502897 0.19154684144863915 chr7 159138663 4396687 0.02762802525241776 0.3723515231358374 chr8 146364022 4053143 0.02769220840351053 0.2313304635863628 chr9 141213431 3322857 0.023530743332764146 0.21324514805396136 chr10 135534747 3740796 0.027600272865820896 0.23250344289085345 chr11 135006516 3601626 0.026677423480804437 0.2375451598980547 chr12 133851895 3500299 0.026150537502662923 0.1781548830211222 chr13 115169878 2494298 0.021657555285419336 0.15798351392346938 chr14 107349540 2428894 0.022626030814850255 0.1691495861558647 chr15 102531392 2265187 0.022092619204857767 0.16075556225496965 chr16 90354753 2343657 0.025938391973690637 0.1825954770594085 chr17 81195210 2123565 0.02615382114289747 0.18946352909267353 chr18 78077248 2147263 0.027501776189652587 0.3960350904150017 chr19 59128983 1575838 0.02665085580788697 0.3130519264546311 chr20 63025520 1691084 0.026831734192752397 0.18173175268365027 chr21 48129895 1067975 0.02218943132953022 0.17662669717562252 chr22 51304566 951520 0.01854649740142037 0.14637758288206845 chrMT 16571 4434 0.26757588558324785 0.55767306468724 chrX 155270560 4479932 0.028852423794955076 0.203446129233308 chrY 59373566 241745 0.004071593072243631 0.10858228581660716