BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819114.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 967,884 number of mapped reads = 827,434 (85.49%) number of supplementary alignments = 2,826 (0.29%) number of secondary alignments = 0 number of mapped bases = 47,471,370 bp number of sequenced bases = 47,456,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,149 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4584 >>>>>>> ACTG content number of A's = 11,968,766 bp (25.22%) number of C's = 9,215,039 bp (19.42%) number of T's = 14,903,670 bp (31.41%) number of G's = 11,368,110 bp (23.95%) number of N's = 587 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 250,504 number of insertions = 3,588 mapped reads with insertion percentage = 0.43% number of deletions = 8,952 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.37% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 0.1751X There is a 1.43% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4504819 0.01807345145992635 0.30327634422882327 chr2 243199373 4111221 0.016904735194362527 0.19877574459261999 chr3 198022430 2473880 0.012492928200103393 0.11817416570802516 chr4 191154276 2966561 0.015519197697675359 0.14089539545061858 chr5 180915260 2749564 0.015198076712821241 0.1299821726115572 chr6 171115067 2131766 0.012458084710915609 0.14712334389678142 chr7 159138663 2389417 0.015014685651845648 0.189986614159934 chr8 146364022 4150362 0.0283564358459622 0.1967907496300699 chr9 141213431 1911258 0.013534534119491792 0.15748021051085245 chr10 135534747 2494010 0.018401259125086205 0.19204277144362542 chr11 135006516 1553623 0.011507763077153994 0.15543331300933041 chr12 133851895 2266784 0.016935016123604377 0.1383890937730804 chr13 115169878 1240415 0.010770307493075577 0.10972767447309943 chr14 107349540 1108915 0.010329946453426815 0.11030836350652029 chr15 102531392 1171847 0.011429153327012278 0.1145602309764765 chr16 90354753 1251832 0.013854633635045186 0.1318379066948934 chr17 81195210 1492331 0.018379544803197135 0.14804022907346576 chr18 78077248 1164736 0.014917738903912186 0.27023717164730204 chr19 59128983 821845 0.01389919052049314 0.21922047819516682 chr20 63025520 1461715 0.023192430621754488 0.16242106923797606 chr21 48129895 637470 0.01324478268651947 0.1310016510154249 chr22 51304566 320033 0.0062379048289776 0.08184584419052388 chrMT 16571 3810 0.22991973930360268 0.49886757242967195 chrX 155270560 2913929 0.018766783606628326 0.156723118243516 chrY 59373566 179227 0.003018632904750912 0.10665256664411561