BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16362020.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 689,432,486 number of mapped reads = 675,218,925 (97.94%) number of supplementary alignments = 28,784,995 (4.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 339,053,542 number of mapped paired reads (second in pair) = 336,165,383 number of mapped paired reads (both in pair) = 670,835,416 number of mapped paired reads (singletons) = 4,383,509 number of mapped bases = 93,887,313,777 bp number of sequenced bases = 93,795,039,830 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 227,270,790 duplication rate = 28.58% >>>>>>> Insert size mean insert size = 80,330.1114 std insert size = 2,763,197.2889 median insert size = 273 >>>>>>> Mapping quality mean mapping quality = 53.9544 >>>>>>> ACTG content number of A's = 27,007,038,330 bp (28.79%) number of C's = 19,761,098,019 bp (21.07%) number of T's = 26,942,695,228 bp (28.73%) number of G's = 20,076,116,694 bp (21.4%) number of N's = 8,091,559 bp (0.01%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 826,271,506 number of insertions = 16,588,590 mapped reads with insertion percentage = 2.32% number of deletions = 55,592,526 mapped reads with deletion percentage = 7.86% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 30.3284X std coverageData = 293.9482X There is a 92.37% of reference with a coverageData >= 1X There is a 92.35% of reference with a coverageData >= 2X There is a 92.32% of reference with a coverageData >= 3X There is a 92.28% of reference with a coverageData >= 4X There is a 92.23% of reference with a coverageData >= 5X There is a 92.15% of reference with a coverageData >= 6X There is a 92.03% of reference with a coverageData >= 7X There is a 91.86% of reference with a coverageData >= 8X There is a 91.63% of reference with a coverageData >= 9X There is a 91.33% of reference with a coverageData >= 10X There is a 90.95% of reference with a coverageData >= 11X There is a 90.48% of reference with a coverageData >= 12X There is a 89.9% of reference with a coverageData >= 13X There is a 89.21% of reference with a coverageData >= 14X There is a 88.39% of reference with a coverageData >= 15X There is a 87.42% of reference with a coverageData >= 16X There is a 86.28% of reference with a coverageData >= 17X There is a 84.94% of reference with a coverageData >= 18X There is a 83.39% of reference with a coverageData >= 19X There is a 81.59% of reference with a coverageData >= 20X There is a 79.54% of reference with a coverageData >= 21X There is a 77.22% of reference with a coverageData >= 22X There is a 74.63% of reference with a coverageData >= 23X There is a 71.77% of reference with a coverageData >= 24X There is a 68.67% of reference with a coverageData >= 25X There is a 65.34% of reference with a coverageData >= 26X There is a 61.82% of reference with a coverageData >= 27X There is a 58.16% of reference with a coverageData >= 28X There is a 54.38% of reference with a coverageData >= 29X There is a 50.55% of reference with a coverageData >= 30X There is a 46.71% of reference with a coverageData >= 31X There is a 42.9% of reference with a coverageData >= 32X There is a 39.17% of reference with a coverageData >= 33X There is a 35.55% of reference with a coverageData >= 34X There is a 32.08% of reference with a coverageData >= 35X There is a 28.79% of reference with a coverageData >= 36X There is a 25.7% of reference with a coverageData >= 37X There is a 22.82% of reference with a coverageData >= 38X There is a 20.16% of reference with a coverageData >= 39X There is a 17.73% of reference with a coverageData >= 40X There is a 15.52% of reference with a coverageData >= 41X There is a 13.53% of reference with a coverageData >= 42X There is a 11.75% of reference with a coverageData >= 43X There is a 10.17% of reference with a coverageData >= 44X There is a 8.78% of reference with a coverageData >= 45X There is a 7.56% of reference with a coverageData >= 46X There is a 6.49% of reference with a coverageData >= 47X There is a 5.57% of reference with a coverageData >= 48X There is a 4.77% of reference with a coverageData >= 49X There is a 4.08% of reference with a coverageData >= 50X There is a 3.5% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7853624453 31.508946382925963 660.8917831697588 chr2 243199373 8094044799 33.28152001033325 258.2014861610991 chr3 198022430 6256267360 31.593730871800734 29.10256396890644 chr4 191154276 6213624187 32.50580796319722 280.02381824256474 chr5 180915260 5682645218 31.410535617614567 26.039158546089162 chr6 171115067 5453647060 31.87122651215746 101.28602113859232 chr7 159138663 5184289142 32.577181712278175 198.57920006645634 chr8 146364022 4710305855 32.182129123234944 411.8944181630074 chr9 141213431 4035385315 28.576497904083926 314.63339589737535 chr10 135534747 4873149501 35.95498282813041 603.3683704593599 chr11 135006516 4304951577 31.886991121228547 87.82043624178601 chr12 133851895 4271525447 31.912327031305757 18.566118137340254 chr13 115169878 2969874193 25.78690057308214 17.564618925550526 chr14 107349540 2867210589 26.709109223942647 24.20413051240122 chr15 102531392 2700999420 26.343145911839372 17.96076132275541 chr16 90354753 2946798986 32.61365770099554 165.03399291076968 chr17 81195210 2772222186 34.14268139709227 129.98252048789158 chr18 78077248 2545511694 32.60247715185863 302.41944774482647 chr19 59128983 2074067888 35.07700932383701 380.5009911817015 chr20 63025520 2009112951 31.877768735585203 78.03713631034822 chr21 48129895 1303822140 27.089652699221556 140.50279671384507 chr22 51304566 1235451877 24.080739265974884 91.0817647959511 chrMT 16571 160070810 9659.695250739243 1308.3419492673752 chrX 155270560 2558416722 16.47715266821991 41.580994924822896 chrY 59373566 810294407 13.647393302938887 331.5861547535333