BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617665.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,114,314 (94.11%) number of supplementary alignments = 141,383 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,123,769 number of mapped paired reads (second in pair) = 14,990,545 number of mapped paired reads (both in pair) = 29,476,694 number of mapped paired reads (singletons) = 637,620 number of mapped bases = 2,924,298,833 bp number of sequenced bases = 2,922,532,868 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,854,828 duplication rate = 10.6% >>>>>>> Insert size mean insert size = 31,517.0967 std insert size = 1,624,033.1136 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.6407 >>>>>>> ACTG content number of A's = 871,650,444 bp (29.83%) number of C's = 582,213,893 bp (19.92%) number of T's = 869,405,105 bp (29.75%) number of G's = 597,522,752 bp (20.45%) number of N's = 1,740,674 bp (0.06%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0156 number of mismatches = 44,558,615 number of insertions = 454,000 mapped reads with insertion percentage = 1.48% number of deletions = 1,069,044 mapped reads with deletion percentage = 3.48% homopolymer indels = 47.67% >>>>>>> Coverage mean coverageData = 0.9446X std coverageData = 10.6961X There is a 33.21% of reference with a coverageData >= 1X There is a 19.23% of reference with a coverageData >= 2X There is a 11.73% of reference with a coverageData >= 3X There is a 7.48% of reference with a coverageData >= 4X There is a 4.92% of reference with a coverageData >= 5X There is a 3.33% of reference with a coverageData >= 6X There is a 2.31% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.88% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% 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 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179039872 0.7183126416363071 10.328364795475906 chr2 243199373 302046649 1.24197133106918 12.168088199631875 chr3 198022430 245609880 1.2403134331802717 2.4721964357609805 chr4 191154276 163773156 0.8567590504750205 8.359738202737441 chr5 180915260 193530630 1.069730823148915 2.3191475302945825 chr6 171115067 141884234 0.8291744057815785 5.820566510081497 chr7 159138663 228773205 1.437571490719386 13.476935305761051 chr8 146364022 129971756 0.888003446639366 4.121219443039816 chr9 141213431 120013171 0.849870795930169 20.702151565983062 chr10 135534747 123892166 0.9140989210685582 21.872418142280925 chr11 135006516 160858262 1.1914851724638238 12.027214822727947 chr12 133851895 124705778 0.9316698728845042 2.1710826516272634 chr13 115169878 126044132 1.0944192543123124 2.2905382179718585 chr14 107349540 83682613 0.7795339691255314 2.4686621417722914 chr15 102531392 62534768 0.6099085048996506 1.580319323974347 chr16 90354753 81309408 0.8998907672294783 16.99539075498007 chr17 81195210 71705046 0.8831191642955293 12.76817119928846 chr18 78077248 53927789 0.6906978714208779 18.429642203097032 chr19 59128983 30743321 0.5199365766192867 6.07461421362619 chr20 63025520 78477084 1.2451636099154755 3.0114274050353704 chr21 48129895 42685379 0.886878706051613 4.396949030579213 chr22 51304566 18633383 0.36319151398727356 1.2621124156036931 chrMT 16571 3084998 186.1684871160461 130.3637396127348 chrX 155270560 145526761 0.9372463202296688 4.327789464166004 chrY 59373566 11845392 0.19950615733607782 17.52147124250521