BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617367.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 = 28,140,411 (87.94%) number of supplementary alignments = 86,699 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,399,829 number of mapped paired reads (second in pair) = 13,740,582 number of mapped paired reads (both in pair) = 27,057,286 number of mapped paired reads (singletons) = 1,083,125 number of mapped bases = 2,734,800,699 bp number of sequenced bases = 2,734,016,607 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,419,834 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 66,271.5566 std insert size = 2,458,779.5891 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.1134 >>>>>>> ACTG content number of A's = 829,089,694 bp (30.32%) number of C's = 541,838,820 bp (19.82%) number of T's = 817,337,065 bp (29.9%) number of G's = 544,685,900 bp (19.92%) number of N's = 1,065,128 bp (0.04%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0165 number of mismatches = 44,405,099 number of insertions = 278,922 mapped reads with insertion percentage = 0.96% number of deletions = 328,779 mapped reads with deletion percentage = 1.13% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 0.8834X std coverageData = 8.6484X There is a 50.51% of reference with a coverageData >= 1X There is a 21.73% of reference with a coverageData >= 2X There is a 7.96% of reference with a coverageData >= 3X There is a 2.68% of reference with a coverageData >= 4X There is a 0.89% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177247596 0.7111219835235636 17.87270632852278 chr2 243199373 270332342 1.1115667720080842 7.741393250627172 chr3 198022430 218149280 1.1016392435947786 1.439027429922178 chr4 191154276 150054144 0.7849897325864685 7.800511895800069 chr5 180915260 172380610 0.9528251513996111 1.379662498993438 chr6 171115067 128674313 0.7519753535204472 3.426903206306749 chr7 159138663 222118552 1.3957547953007499 10.010398316095017 chr8 146364022 115207346 0.7871288614902916 6.469147469919091 chr9 141213431 114776180 0.8127851521432122 12.426724730244985 chr10 135534747 114764323 0.846752036214005 17.992748656257493 chr11 135006516 146577982 1.085710426006401 4.8143709943955 chr12 133851895 120887789 0.9031458912105802 1.3083675424990096 chr13 115169878 119699795 1.0393324806682525 1.271797857498796 chr14 107349540 79237376 0.7381249700743944 1.3021593691967706 chr15 102531392 61622062 0.6010067823910944 1.0831355203047894 chr16 90354753 68466279 0.7577496116889391 7.3550354255560455 chr17 81195210 84343097 1.038769368291553 6.1753300743345605 chr18 78077248 49232481 0.63056117193065 13.21564117809656 chr19 59128983 50294026 0.8505816174785215 8.763166829750446 chr20 63025520 77970425 1.2371246599790053 2.1472248424218234 chr21 48129895 43443502 0.902630309083367 2.863565110439223 chr22 51304566 24046722 0.4687053000311902 0.881149223368695 chrMT 16571 1846347 111.4203729406795 20.37517225555858 chrX 155270560 114399477 0.7367750654084071 2.6984043104867754 chrY 59373566 9028653 0.1520651968251326 7.065831535387839