BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365363.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 859,328,356 number of mapped reads = 778,937,010 (90.64%) number of supplementary alignments = 75,887,493 (8.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 389,035,804 number of mapped paired reads (second in pair) = 389,901,206 number of mapped paired reads (both in pair) = 771,035,106 number of mapped paired reads (singletons) = 7,901,904 number of mapped bases = 102,589,068,786 bp number of sequenced bases = 102,467,813,261 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 494,344,827 duplication rate = 39.35% >>>>>>> Insert size mean insert size = 139,588.9463 std insert size = 3,127,472.9343 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 53.0794 >>>>>>> ACTG content number of A's = 28,462,727,289 bp (27.78%) number of C's = 22,842,499,518 bp (22.29%) number of T's = 27,701,709,558 bp (27.03%) number of G's = 23,450,329,417 bp (22.89%) number of N's = 10,547,479 bp (0.01%) GC percentage = 45.18% >>>>>>> Mismatches and indels general error rate = 0.0157 number of mismatches = 1,464,462,260 number of insertions = 33,497,038 mapped reads with insertion percentage = 3.88% number of deletions = 29,961,731 mapped reads with deletion percentage = 3.5% homopolymer indels = 36.04% >>>>>>> Coverage mean coverageData = 33.1393X std coverageData = 940.3496X There is a 83.88% of reference with a coverageData >= 1X There is a 81.43% of reference with a coverageData >= 2X There is a 76.22% of reference with a coverageData >= 3X There is a 73.53% of reference with a coverageData >= 4X There is a 69.36% of reference with a coverageData >= 5X There is a 66.65% of reference with a coverageData >= 6X There is a 63.19% of reference with a coverageData >= 7X There is a 60.62% of reference with a coverageData >= 8X There is a 57.69% of reference with a coverageData >= 9X There is a 55.32% of reference with a coverageData >= 10X There is a 52.79% of reference with a coverageData >= 11X There is a 50.63% of reference with a coverageData >= 12X There is a 48.43% of reference with a coverageData >= 13X There is a 46.47% of reference with a coverageData >= 14X There is a 44.53% of reference with a coverageData >= 15X There is a 42.77% of reference with a coverageData >= 16X There is a 41.05% of reference with a coverageData >= 17X There is a 39.46% of reference with a coverageData >= 18X There is a 37.92% of reference with a coverageData >= 19X There is a 36.49% of reference with a coverageData >= 20X There is a 35.11% of reference with a coverageData >= 21X There is a 33.82% of reference with a coverageData >= 22X There is a 32.58% of reference with a coverageData >= 23X There is a 31.41% of reference with a coverageData >= 24X There is a 30.29% of reference with a coverageData >= 25X There is a 29.23% of reference with a coverageData >= 26X There is a 28.21% of reference with a coverageData >= 27X There is a 27.25% of reference with a coverageData >= 28X There is a 26.33% of reference with a coverageData >= 29X There is a 25.45% of reference with a coverageData >= 30X There is a 24.61% of reference with a coverageData >= 31X There is a 23.81% of reference with a coverageData >= 32X There is a 23.04% of reference with a coverageData >= 33X There is a 22.3% of reference with a coverageData >= 34X There is a 21.6% of reference with a coverageData >= 35X There is a 20.93% of reference with a coverageData >= 36X There is a 20.28% of reference with a coverageData >= 37X There is a 19.67% of reference with a coverageData >= 38X There is a 19.07% of reference with a coverageData >= 39X There is a 18.5% of reference with a coverageData >= 40X There is a 17.96% of reference with a coverageData >= 41X There is a 17.43% of reference with a coverageData >= 42X There is a 16.93% of reference with a coverageData >= 43X There is a 16.45% of reference with a coverageData >= 44X There is a 15.98% of reference with a coverageData >= 45X There is a 15.53% of reference with a coverageData >= 46X There is a 15.1% of reference with a coverageData >= 47X There is a 14.69% of reference with a coverageData >= 48X There is a 14.29% of reference with a coverageData >= 49X There is a 13.9% of reference with a coverageData >= 50X There is a 13.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7425290141 29.790457938317434 441.6744004343573 chr2 243199373 7257492946 29.841742009754277 535.6289036787553 chr3 198022430 5516583275 27.858375816315355 212.00828283169713 chr4 191154276 6321522451 33.070264413023125 1607.5717191885856 chr5 180915260 4603455016 25.44536605701476 83.17433980585145 chr6 171115067 4689681463 27.4065957207614 328.0142473716644 chr7 159138663 4824048161 30.31348931843169 187.9015270832634 chr8 146364022 4003524963 27.35320407497411 143.61278976894107 chr9 141213431 3686393671 26.10512077282507 401.5997180502338 chr10 135534747 7241609159 53.4299087082075 2303.4174614093786 chr11 135006516 4295956645 31.820365211113216 153.70477890744857 chr12 133851895 3776984527 28.217639556018238 102.7626893797918 chr13 115169878 1945948693 16.896333718439816 33.60758520957665 chr14 107349540 2631597635 24.514288882840113 81.1343870283492 chr15 102531392 2508493654 24.46561589644662 53.400755297452775 chr16 90354753 5653921777 62.574702373432416 1379.8264348912862 chr17 81195210 3564612064 43.90175312065823 734.5227840978955 chr18 78077248 2762408341 35.380452202926 1936.6952046981207 chr19 59128983 3096541008 52.369258710233524 330.7410684930904 chr20 63025520 2216640644 35.170525272937056 624.1309779943284 chr21 48129895 1988981367 41.32527957935499 1005.9274047954506 chr22 51304566 1761669411 34.3374780911313 110.99350959812773 chrMT 16571 61713213 3724.169513004647 2002.7996539273806 chrX 155270560 2433964092 15.675631568534305 159.3311218572454 chrY 59373566 8320034469 140.13028068753695 3544.4655416414525