BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365373.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 = 545,164,294 number of mapped reads = 512,912,537 (94.08%) number of supplementary alignments = 10,928,236 (2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 256,874,333 number of mapped paired reads (second in pair) = 256,038,204 number of mapped paired reads (both in pair) = 507,137,432 number of mapped paired reads (singletons) = 5,775,105 number of mapped bases = 70,737,630,235 bp number of sequenced bases = 70,723,100,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,072,872 duplication rate = 36.88% >>>>>>> Insert size mean insert size = 90,737.3894 std insert size = 2,996,923.1625 median insert size = 160 >>>>>>> Mapping quality mean mapping quality = 54.3865 >>>>>>> ACTG content number of A's = 19,150,725,706 bp (27.08%) number of C's = 16,291,054,712 bp (23.03%) number of T's = 18,449,970,065 bp (26.09%) number of G's = 16,829,703,733 bp (23.8%) number of N's = 1,645,838 bp (0%) GC percentage = 46.83% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 421,613,938 number of insertions = 6,369,417 mapped reads with insertion percentage = 1.21% number of deletions = 4,994,050 mapped reads with deletion percentage = 0.94% homopolymer indels = 41.55% >>>>>>> Coverage mean coverageData = 22.8503X std coverageData = 46.3744X There is a 80.2% of reference with a coverageData >= 1X There is a 77.7% of reference with a coverageData >= 2X There is a 71.17% of reference with a coverageData >= 3X There is a 68.5% of reference with a coverageData >= 4X There is a 63.83% of reference with a coverageData >= 5X There is a 61.25% of reference with a coverageData >= 6X There is a 57.67% of reference with a coverageData >= 7X There is a 55.29% of reference with a coverageData >= 8X There is a 52.41% of reference with a coverageData >= 9X There is a 50.26% of reference with a coverageData >= 10X There is a 47.86% of reference with a coverageData >= 11X There is a 45.93% of reference with a coverageData >= 12X There is a 43.89% of reference with a coverageData >= 13X There is a 42.15% of reference with a coverageData >= 14X There is a 40.39% of reference with a coverageData >= 15X There is a 38.83% of reference with a coverageData >= 16X There is a 37.28% of reference with a coverageData >= 17X There is a 35.88% of reference with a coverageData >= 18X There is a 34.5% of reference with a coverageData >= 19X There is a 33.24% of reference with a coverageData >= 20X There is a 32.01% of reference with a coverageData >= 21X There is a 30.87% of reference with a coverageData >= 22X There is a 29.77% of reference with a coverageData >= 23X There is a 28.73% of reference with a coverageData >= 24X There is a 27.73% of reference with a coverageData >= 25X There is a 26.79% of reference with a coverageData >= 26X There is a 25.88% of reference with a coverageData >= 27X There is a 25.02% of reference with a coverageData >= 28X There is a 24.2% of reference with a coverageData >= 29X There is a 23.41% of reference with a coverageData >= 30X There is a 22.65% of reference with a coverageData >= 31X There is a 21.93% of reference with a coverageData >= 32X There is a 21.24% of reference with a coverageData >= 33X There is a 20.58% of reference with a coverageData >= 34X There is a 19.94% of reference with a coverageData >= 35X There is a 19.33% of reference with a coverageData >= 36X There is a 18.75% of reference with a coverageData >= 37X There is a 18.19% of reference with a coverageData >= 38X There is a 17.64% of reference with a coverageData >= 39X There is a 17.13% of reference with a coverageData >= 40X There is a 16.63% of reference with a coverageData >= 41X There is a 16.15% of reference with a coverageData >= 42X There is a 15.68% of reference with a coverageData >= 43X There is a 15.24% of reference with a coverageData >= 44X There is a 14.81% of reference with a coverageData >= 45X There is a 14.4% of reference with a coverageData >= 46X There is a 14% of reference with a coverageData >= 47X There is a 13.61% of reference with a coverageData >= 48X There is a 13.24% of reference with a coverageData >= 49X There is a 12.89% of reference with a coverageData >= 50X There is a 12.54% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6436143887 25.82197733822296 52.56326168076084 chr2 243199373 6155566555 25.3107829969611 68.95179513501752 chr3 198022430 4787419876 24.176149520031643 38.32430401234335 chr4 191154276 4022105480 21.041148354954927 41.866914652779045 chr5 180915260 4157363433 22.979617269433213 41.31177691700581 chr6 171115067 4228918311 24.71388630552329 43.951301782637586 chr7 159138663 3913794615 24.593612521427303 43.04562819199735 chr8 146364022 3589472995 24.524285039119793 43.951768458567365 chr9 141213431 3054927159 21.633403688067038 40.51737893137636 chr10 135534747 3509470639 25.893512303527597 50.186742862742776 chr11 135006516 3419553784 25.328805492617853 42.68687103989988 chr12 133851895 3325009608 24.840960286740803 43.61420569025666 chr13 115169878 1980061274 17.192527320381462 32.289353841602875 chr14 107349540 2126933671 19.813160550105756 38.65969723959396 chr15 102531392 2191214274 21.3711550312318 42.06431878330116 chr16 90354753 2192835656 24.26917880014569 43.330972104566825 chr17 81195210 2099955930 25.86305189678061 52.080678788456574 chr18 78077248 1788881909 22.911692648285964 54.69584238011733 chr19 59128983 1684004887 28.48019366407841 56.14839250863319 chr20 63025520 1722854878 27.33582964488036 50.297291347538184 chr21 48129895 808458978 16.797439055289857 42.12458226944454 chr22 51304566 1044363930 20.356159527789398 50.3356443456996 chrMT 16571 2919623 176.1887031561161 84.52778376921641 chrX 155270560 2147004225 13.827503584710456 30.68490495183641 chrY 59373566 348394658 5.86784122078839 29.84853679488038