BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524543.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 = 1,215,471 number of mapped reads = 1,123,292 (92.42%) number of supplementary alignments = 4,700 (0.39%) number of secondary alignments = 0 number of mapped bases = 66,248,307 bp number of sequenced bases = 66,227,970 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,204 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9903 >>>>>>> ACTG content number of A's = 17,061,475 bp (25.76%) number of C's = 12,022,130 bp (18.15%) number of T's = 20,511,574 bp (30.97%) number of G's = 16,631,711 bp (25.11%) number of N's = 1,080 bp (0%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 323,861 number of insertions = 3,726 mapped reads with insertion percentage = 0.33% number of deletions = 12,114 mapped reads with deletion percentage = 1.07% homopolymer indels = 44.46% >>>>>>> Coverage mean coverageData = 0.0214X std coverageData = 0.209X There is a 1.95% of reference with a coverageData >= 1X There is a 0.14% 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 5379497 0.021582682435924604 0.35519513708102274 chr2 243199373 5484822 0.022552780183360096 0.23207849081184553 chr3 198022430 4326820 0.021850151015720794 0.15911268336603315 chr4 191154276 4240241 0.02218229740254411 0.17740619768484797 chr5 180915260 3946370 0.021813361681043378 0.159281023629336 chr6 171115067 3827676 0.022369017919386374 0.17876745439440417 chr7 159138663 3611340 0.02269303971719305 0.24733576053672743 chr8 146364022 3408799 0.023289869692156996 0.22157094221356505 chr9 141213431 2745675 0.01944344090046222 0.1791512324560474 chr10 135534747 3210665 0.02368886998401967 0.20532868463148302 chr11 135006516 3039859 0.02251638728311454 0.1990264986673555 chr12 133851895 2911162 0.021749128019442683 0.1597907704072184 chr13 115169878 2062564 0.01790888412680267 0.14378700686944523 chr14 107349540 2014637 0.01876707622594377 0.14929688541273556 chr15 102531392 1951184 0.019030113235954115 0.1489637986430065 chr16 90354753 1953491 0.021620235074960584 0.16579690083374926 chr17 81195210 1823258 0.02245524089413649 0.17096010935852118 chr18 78077248 1795226 0.0229929466776288 0.32783694071210256 chr19 59128983 1371033 0.02318715679584748 0.24647030293950037 chr20 63025520 1462655 0.02320734521508113 0.16586689776660987 chr21 48129895 911106 0.018930147260865622 0.16686189983159289 chr22 51304566 809419 0.015776743925677104 0.13490566164536769 chrMT 16571 7883 0.4757105787218635 0.7639426171158564 chrX 155270560 3740284 0.024088816321651704 0.17900388240710363 chrY 59373566 212641 0.0035814086019357503 0.11632742921748591