BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926895.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 33,307,972 number of mapped reads = 23,075,028 (69.28%) number of supplementary alignments = 553,861 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,535,818 number of mapped paired reads (second in pair) = 11,539,210 number of mapped paired reads (both in pair) = 22,316,122 number of mapped paired reads (singletons) = 758,906 number of mapped bases = 2,004,045,969 bp number of sequenced bases = 2,002,459,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,809,947 duplication rate = 9.74% >>>>>>> Insert size mean insert size = 250,839.2019 std insert size = 4,973,522.5517 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 52.5104 >>>>>>> ACTG content number of A's = 563,775,494 bp (28.15%) number of C's = 379,148,902 bp (18.93%) number of T's = 581,536,413 bp (29.04%) number of G's = 477,771,026 bp (23.86%) number of N's = 227,442 bp (0.01%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 19,896,518 number of insertions = 337,023 mapped reads with insertion percentage = 1.44% number of deletions = 1,072,348 mapped reads with deletion percentage = 4.53% homopolymer indels = 51.72% >>>>>>> Coverage mean coverageData = 0.6474X std coverageData = 2.6871X There is a 28.07% of reference with a coverageData >= 1X There is a 14.18% of reference with a coverageData >= 2X There is a 7.63% of reference with a coverageData >= 3X There is a 4.56% of reference with a coverageData >= 4X There is a 2.86% of reference with a coverageData >= 5X There is a 1.89% of reference with a coverageData >= 6X There is a 1.29% of reference with a coverageData >= 7X There is a 0.9% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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% 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 168632571 0.6765582782640289 2.0717488967698334 chr2 243199373 176788055 0.7269264423638132 6.719805695568388 chr3 198022430 138771089 0.7007846989858674 1.6402132165123935 chr4 191154276 122641652 0.6415846643158535 1.7548451207755378 chr5 180915260 122974521 0.6797354794725442 1.5930156651504042 chr6 171115067 117915229 0.6890990435108791 1.7332226305370617 chr7 159138663 105206720 0.6611009418873903 1.8285266952702846 chr8 146364022 103667235 0.7082835903484532 1.6986920842517361 chr9 141213431 86070261 0.6095047786212346 2.0779166526811843 chr10 135534747 98824928 0.7291482825433687 4.457648622823801 chr11 135006516 97312181 0.7207961799414185 1.8371275018882542 chr12 133851895 93117791 0.6956777937286581 1.7350202412973588 chr13 115169878 61207622 0.5314551257925271 1.4253167528294015 chr14 107349540 61365657 0.5716434089983059 1.555678051011042 chr15 102531392 60730127 0.5923076417415654 1.5821119263587669 chr16 90354753 33079527 0.36610721518988604 2.2639888172170877 chr17 81195210 52398771 0.6453431304629916 1.6818170668072574 chr18 78077248 52230179 0.6689551737274346 2.014306023383976 chr19 59128983 33511178 0.5667470722437421 1.6191309856455136 chr20 63025520 47546323 0.7543979486404873 1.8007064240661461 chr21 48129895 23000186 0.4778773359052622 1.8970177020671923 chr22 51304566 25637707 0.4997158927336019 1.5079590203069648 chrMT 16571 57990 3.499487055699716 3.4561719640282806 chrX 155270560 118098225 0.7605963744833535 1.7767830885592224 chrY 59373566 3260244 0.054910698811656354 1.5833970900217675