BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006194.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 2,981,672 number of mapped reads = 2,599,323 (87.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,302,388 number of mapped paired reads (second in pair) = 1,296,935 number of mapped paired reads (both in pair) = 2,407,984 number of mapped paired reads (singletons) = 191,339 number of mapped bases = 100,572,467 bp number of sequenced bases = 100,558,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,904 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 50,441.4776 std insert size = 2,097,956.5676 median insert size = 113 >>>>>>> Mapping quality mean mapping quality = 47.8421 >>>>>>> ACTG content number of A's = 27,634,548 bp (27.48%) number of C's = 21,913,862 bp (21.79%) number of T's = 28,235,695 bp (28.08%) number of G's = 22,770,013 bp (22.64%) number of N's = 4,805 bp (0%) GC percentage = 44.44% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 294,431 number of insertions = 3,319 mapped reads with insertion percentage = 0.13% number of deletions = 10,133 mapped reads with deletion percentage = 0.39% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 0.2319X There is a 2.81% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8443076 0.03387384138152258 0.27790323082337925 chr2 243199373 8527466 0.035063684148560696 0.2333236488990113 chr3 198022430 6785143 0.034264517408457214 0.20698730349534142 chr4 191154276 6167676 0.032265435694464925 0.21049772862880012 chr5 180915260 5978352 0.03304503998170193 0.20319639895258812 chr6 171115067 5526919 0.03229942924897432 0.2106052168167621 chr7 159138663 5405535 0.03396745264851195 0.25997726179297287 chr8 146364022 5019306 0.03429330467565315 0.3230616601004487 chr9 141213431 4218049 0.029870027023137763 0.2109218494973952 chr10 135534747 4817120 0.03554158698507033 0.24582385018231132 chr11 135006516 4572303 0.033867276450567765 0.22664174271945087 chr12 133851895 4567009 0.034119868082554974 0.20707576579016915 chr13 115169878 3038157 0.02637978829846464 0.18132082126761112 chr14 107349540 3097872 0.028857804141498883 0.2792569513576012 chr15 102531392 2923112 0.028509434456912473 0.1893662729312575 chr16 90354753 3140575 0.03475827110058062 0.22235745588977482 chr17 81195210 2897145 0.035681230456821283 0.2175775328440656 chr18 78077248 2561589 0.03280839252940882 0.27837776579191975 chr19 59128983 2266767 0.03833597137972084 0.25283631327098116 chr20 63025520 2299661 0.036487775110780524 0.21723737121862616 chr21 48129895 1318690 0.027398563824001694 0.20392552164272193 chr22 51304566 1332242 0.025967318386437573 0.1927343328885015 chrMT 16571 1257 0.07585541005370829 0.38117314517427 chrX 155270560 5424809 0.034937782152650185 0.2158457269877375 chrY 59373566 242637 0.004086616592980115 0.1006897082394639