BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080720.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,364,986 number of mapped reads = 2,120,525 (89.66%) number of supplementary alignments = 13,276 (0.56%) number of secondary alignments = 0 number of mapped bases = 142,335,359 bp number of sequenced bases = 142,284,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,388 duplication rate = 4.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0671 >>>>>>> ACTG content number of A's = 39,434,854 bp (27.72%) number of C's = 26,158,488 bp (18.38%) number of T's = 45,477,519 bp (31.96%) number of G's = 31,211,203 bp (21.94%) number of N's = 2,044 bp (0%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,171,931 number of insertions = 10,170 mapped reads with insertion percentage = 0.48% number of deletions = 29,300 mapped reads with deletion percentage = 1.37% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.3801X There is a 3.77% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% 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 16632877 0.0667315368494107 0.49450908596687987 chr2 243199373 9602844 0.03948548008797704 0.3920520378276663 chr3 198022430 9167572 0.04629562418762359 0.2503246241656493 chr4 191154276 6003918 0.03140875593073314 0.21108547485829793 chr5 180915260 6451343 0.03565947394376793 0.21896835077631047 chr6 171115067 8560729 0.05002907780178118 0.3749201099217563 chr7 159138663 9313584 0.05852496071303553 0.9543902290155408 chr8 146364022 17397737 0.11886621290032601 0.5239836212595504 chr9 141213431 4307172 0.030501149710044223 0.27543659597737297 chr10 135534747 6665448 0.049178886946238225 0.3291165234692953 chr11 135006516 5891088 0.043635582744761744 0.28073361043743883 chr12 133851895 4578666 0.03420695687573194 0.21820730761136475 chr13 115169878 2979717 0.025872363952664776 0.18853003225345114 chr14 107349540 2934309 0.02733415532101954 0.20335065298360677 chr15 102531392 2467081 0.02406171370422826 0.1823361625996854 chr16 90354753 3640076 0.04028649162485121 0.25097976147522705 chr17 81195210 2149802 0.026476955968215365 0.19858833907071094 chr18 78077248 4507233 0.057727867150235625 0.41823589900988006 chr19 59128983 2340809 0.03958818300663145 0.34384662411439215 chr20 63025520 3661276 0.05809196020913433 0.2873800046182742 chr21 48129895 2088471 0.04339238637441449 0.25179976210181426 chr22 51304566 1296303 0.025266815433152675 0.18334312915805345 chrMT 16571 29663 1.7900549152133245 1.7700323082043548 chrX 155270560 9366851 0.06032599483121591 0.30196198002817964 chrY 59373566 300790 0.0050660591954338734 0.10138692451389814