BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080946.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 = 3,152,156 number of mapped reads = 2,816,455 (89.35%) number of supplementary alignments = 24,119 (0.77%) number of secondary alignments = 0 number of mapped bases = 193,094,739 bp number of sequenced bases = 193,023,455 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,919 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6947 >>>>>>> ACTG content number of A's = 55,574,451 bp (28.79%) number of C's = 34,139,836 bp (17.69%) number of T's = 61,824,760 bp (32.03%) number of G's = 40,556,566 bp (21.01%) number of N's = 927,842 bp (0.48%) GC percentage = 38.7% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 2,194,110 number of insertions = 15,119 mapped reads with insertion percentage = 0.53% number of deletions = 43,303 mapped reads with deletion percentage = 1.52% homopolymer indels = 49.7% >>>>>>> Coverage mean coverageData = 0.0624X std coverageData = 0.5333X There is a 4.93% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15018145 0.060253189900778624 0.9098111726339051 chr2 243199373 16563401 0.06810626522462293 0.48621717081296006 chr3 198022430 13495753 0.06815264816212992 0.31507130093806995 chr4 191154276 13733562 0.07184543441759053 0.34158879168817363 chr5 180915260 12306416 0.06802309545363945 0.31622689109406876 chr6 171115067 11712357 0.06844725718980667 0.41951983447971464 chr7 159138663 10896695 0.06847295807681883 0.8074663378608629 chr8 146364022 10174487 0.06951494541465934 0.9997037236405001 chr9 141213431 8121377 0.057511363773889185 0.5008162883351168 chr10 135534747 8656384 0.06386837465377052 0.4485385349528169 chr11 135006516 8863641 0.06565343112772423 0.4665597710132501 chr12 133851895 8661865 0.06471230758443876 0.31343855304421747 chr13 115169878 6659277 0.05782134283410459 0.28920547498772436 chr14 107349540 5964305 0.05555966984115628 0.31243501617610236 chr15 102531392 5172423 0.05044721327883659 0.27092196235476856 chr16 90354753 4667789 0.05166069127542189 0.3079358408674074 chr17 81195210 4230636 0.05210450222371492 0.31805231364290654 chr18 78077248 5324265 0.06819227286289599 0.9090223540509939 chr19 59128983 2899445 0.04903593555803251 0.6544749656747701 chr20 63025520 3483941 0.05527825871170916 0.2988826845475758 chr21 48129895 2566614 0.05332681486215584 0.30614677113236055 chr22 51304566 1686549 0.032873272916878395 0.2134139872513534 chrMT 16571 52774 3.1847202944903747 2.761088666649941 chrX 155270560 11730247 0.0755471417118609 0.37654651400579536 chrY 59373566 452391 0.00761940086266673 0.16701902452900602