BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085041.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 = 1,925,390 number of mapped reads = 1,686,842 (87.61%) number of supplementary alignments = 12,004 (0.62%) number of secondary alignments = 0 number of mapped bases = 116,144,437 bp number of sequenced bases = 116,099,112 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,694 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7459 >>>>>>> ACTG content number of A's = 34,324,716 bp (29.57%) number of C's = 21,274,239 bp (18.32%) number of T's = 36,495,800 bp (31.44%) number of G's = 23,991,143 bp (20.66%) number of N's = 13,214 bp (0.01%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,040,242 number of insertions = 8,936 mapped reads with insertion percentage = 0.53% number of deletions = 26,177 mapped reads with deletion percentage = 1.53% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.3512X There is a 3.32% of reference with a coverageData >= 1X There is a 0.32% 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 9552799 0.038326079035125055 0.5055516649105775 chr2 243199373 11427767 0.046989294664012145 0.34295607033848735 chr3 198022430 8454027 0.042692269759541886 0.2332322739307093 chr4 191154276 7284776 0.038109406456594254 0.21781164446495607 chr5 180915260 5714567 0.03158698166202232 0.1949822801827668 chr6 171115067 7492825 0.04378822468041344 0.2856499246509058 chr7 159138663 9792105 0.06153190441219177 0.3218872281055943 chr8 146364022 6614609 0.04519286167197564 0.9156885979021909 chr9 141213431 3655413 0.02588573178991735 0.26558341872292635 chr10 135534747 8535586 0.06297710505188754 0.45518000055989116 chr11 135006516 5269817 0.03903379745019122 0.3138897804716092 chr12 133851895 5017096 0.03748244281487386 0.215110140309842 chr13 115169878 2456951 0.021333277786401754 0.1588526535242392 chr14 107349540 4496974 0.041890948018966825 0.23085690881520587 chr15 102531392 2281905 0.022255671706866126 0.16348871658347464 chr16 90354753 2750316 0.030439084925615367 0.20257996798409425 chr17 81195210 1644803 0.020257389567685087 0.1788203489940657 chr18 78077248 2854883 0.03656485177346415 0.4369160676619391 chr19 59128983 1469279 0.02484871082595823 0.32642114701593267 chr20 63025520 2068242 0.032815945033059624 0.19992919751838836 chr21 48129895 1357090 0.02819640475010386 0.1906144064831625 chr22 51304566 556307 0.01084322592262061 0.11193818316622131 chrMT 16571 3972 0.23969585420312595 0.5130255236412745 chrX 155270560 5176443 0.03333821298770353 0.2187525508985514 chrY 59373566 215885 0.003636045710981887 0.08207793519001608