BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548928.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,398,625 number of mapped reads = 4,728,859 (87.59%) number of secondary alignments = 0 number of mapped bases = 187,648,129 bp number of sequenced bases = 187,630,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,840 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6344 >>>>>>> ACTG content number of A's = 54,156,851 bp (28.86%) number of C's = 39,350,244 bp (20.97%) number of T's = 54,641,720 bp (29.12%) number of G's = 39,479,523 bp (21.04%) number of N's = 1,677 bp (0%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 445,616 number of insertions = 4,583 mapped reads with insertion percentage = 0.1% number of deletions = 13,516 mapped reads with deletion percentage = 0.29% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0606X std coverageData = 0.4753X There is a 5.01% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15275731 0.06128663165898391 0.6304362356589546 chr2 243199373 16148215 0.06639908154697421 0.3584363460624662 chr3 198022430 11905420 0.060121573096542646 0.2875798132103606 chr4 191154276 11876541 0.062130658275203844 0.2968902186112542 chr5 180915260 11746070 0.06492581112284282 0.2995897827154513 chr6 171115067 10427267 0.06093716458060353 0.31275393032691906 chr7 159138663 10065550 0.06325018578294829 0.4777470150490814 chr8 146364022 9238647 0.06312102437305256 1.3918256069078396 chr9 141213431 7989320 0.05657620485122269 0.34768853061525506 chr10 135534747 8359656 0.06167906153246444 0.33908997390854023 chr11 135006516 8757959 0.06487063928084774 0.40043454269172396 chr12 133851895 9044461 0.06757066084122305 0.30778862332308043 chr13 115169878 5961522 0.051762857645816035 0.26459246405424103 chr14 107349540 6252990 0.05824887558903373 0.3009269604468068 chr15 102531392 5922364 0.05776147075034346 0.27993410443263794 chr16 90354753 5564606 0.061586201226182316 0.30577606373331434 chr17 81195210 5110074 0.06293565839659754 0.3035810361930067 chr18 78077248 5139689 0.06582825511472945 0.5661219041906855 chr19 59128983 3891533 0.06581430632757543 0.5502426599094973 chr20 63025520 4106845 0.06516162024525939 0.303466717152825 chr21 48129895 2446957 0.05084068851594212 0.27985891451293565 chr22 51304566 2323608 0.045290471807129216 0.25713118935366935 chrMT 16571 13411 0.8093054130710277 1.4041372076002587 chrX 155270560 9563004 0.06158929290910009 0.3289698902233328 chrY 59373566 516689 0.008702340701584271 0.14216455100710482