BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013347.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 = 1,832,344 number of mapped reads = 289,529 (15.8%) number of supplementary alignments = 3,706 (0.2%) number of secondary alignments = 0 number of mapped bases = 18,282,874 bp number of sequenced bases = 18,273,744 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,489 duplication rate = 14.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0858 >>>>>>> ACTG content number of A's = 4,956,968 bp (27.13%) number of C's = 3,287,834 bp (17.99%) number of T's = 5,908,300 bp (32.33%) number of G's = 4,118,544 bp (22.54%) number of N's = 2,098 bp (0.01%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 152,491 number of insertions = 1,426 mapped reads with insertion percentage = 0.48% number of deletions = 5,392 mapped reads with deletion percentage = 1.84% homopolymer indels = 45.23% >>>>>>> Coverage mean coverageData = 0.0059X std coverageData = 0.1918X There is a 0.22% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 1221091 0.004899048977695426 0.1668829128825946 chr2 243199373 2266139 0.009318029779624473 0.2506317462590368 chr3 198022430 808624 0.0040834970058694865 0.1542647451656869 chr4 191154276 885108 0.0046303332497777865 0.15482779891060966 chr5 180915260 942545 0.005209870079505731 0.1680391478520627 chr6 171115067 2447103 0.014300920678130583 0.3092758039335844 chr7 159138663 1227268 0.007711941126462775 0.2586808264913259 chr8 146364022 625595 0.004274240291101046 0.154659744641851 chr9 141213431 579040 0.004100459820992523 0.1496020433794735 chr10 135534747 842093 0.00621311522424578 0.18240728732863648 chr11 135006516 523149 0.003874990744891158 0.1348909075118003 chr12 133851895 626497 0.004680523947755839 0.1571856081358806 chr13 115169878 595369 0.005169485375333991 0.16929445692397221 chr14 107349540 669241 0.006234223267281816 0.19092442075879695 chr15 102531392 416716 0.004064277211802606 0.15319117927197018 chr16 90354753 371668 0.004113430535303439 0.14659667638249319 chr17 81195210 435217 0.005360131465883271 0.16675238597089304 chr18 78077248 480997 0.006160527071855811 0.29720652046866464 chr19 59128983 259754 0.004393006387409031 0.1469036799657609 chr20 63025520 277295 0.004399725698415499 0.1484213901182551 chr21 48129895 239599 0.004978174168050855 0.15904343925993783 chr22 51304566 147176 0.0028686725466111535 0.11889409661595467 chrMT 16571 15233 0.91925653249653 2.1739400991047395 chrX 155270560 1325383 0.008535958136558533 0.2229650840140301 chrY 59373566 54974 9.259002566899889E-4 0.048094551424460036