BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354878.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 20,677,640 number of mapped reads = 20,582,377 (99.54%) number of supplementary alignments = 113,448 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,295,848 number of mapped paired reads (second in pair) = 10,286,529 number of mapped paired reads (both in pair) = 20,541,954 number of mapped paired reads (singletons) = 40,423 number of mapped bases = 3,055,339,880 bp number of sequenced bases = 3,054,028,774 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,222,636 duplication rate = 23.34% >>>>>>> Insert size mean insert size = 38,275.3528 std insert size = 1,928,375.1322 median insert size = 303 >>>>>>> Mapping quality mean mapping quality = 54.49 >>>>>>> ACTG content number of A's = 873,312,478 bp (28.6%) number of C's = 653,685,066 bp (21.4%) number of T's = 868,516,284 bp (28.44%) number of G's = 658,474,110 bp (21.56%) number of N's = 40,836 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 17,408,598 number of insertions = 452,972 mapped reads with insertion percentage = 2.05% number of deletions = 458,000 mapped reads with deletion percentage = 2.12% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.987X std coverageData = 11.8008X There is a 46.84% of reference with a coverageData >= 1X There is a 24.81% of reference with a coverageData >= 2X There is a 11.69% of reference with a coverageData >= 3X There is a 5.68% of reference with a coverageData >= 4X There is a 2.59% of reference with a coverageData >= 5X There is a 1.26% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 258118621 1.0355786475653355 27.35576308807622 chr2 243199373 260761324 1.0722121557443325 8.62838056208662 chr3 198022430 195977301 0.989672235614925 1.4969358743987107 chr4 191154276 190575814 0.9969738474487487 10.160719444211328 chr5 180915260 178087063 0.9843672833347502 1.5697593962832717 chr6 171115067 169755577 0.9920551122479472 3.9556088953716113 chr7 159138663 168524396 1.0589783326255544 13.506654362775645 chr8 146364022 149518312 1.0215509929072597 5.865418906363248 chr9 141213431 134814471 0.954685896697744 17.639689160146187 chr10 135534747 164761381 1.215639418281424 24.166829746746146 chr11 135006516 143161240 1.0604024475381617 5.438463252576437 chr12 133851895 135879950 1.0151514851545433 1.6655502943007987 chr13 115169878 91615604 0.7954823395749364 1.3237123519232892 chr14 107349540 93453740 0.8705555701496253 1.525489874922618 chr15 102531392 89940080 0.8771955422198892 1.386991383095199 chr16 90354753 102640292 1.1359700357987808 4.611543241991279 chr17 81195210 98578062 1.2140871610529735 7.040003512201959 chr18 78077248 83089790 1.0641997781479182 12.87625692494737 chr19 59128983 75191116 1.2716456834713359 12.303962305047612 chr20 63025520 70410852 1.1171800248534245 3.883969156865585 chr21 48129895 43132766 0.8961741138226045 5.191678757869676 chr22 51304566 45398262 0.8848776149865492 2.613030476095753 chrMT 16571 4651880 280.7241566592239 33.2929231951368 chrX 155270560 77981058 0.5022269385774096 2.122071435967609 chrY 59373566 29320928 0.49383808275891666 11.932827442115412