BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084413.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 = 2,590,819 number of mapped reads = 2,285,888 (88.23%) number of supplementary alignments = 27,086 (1.05%) number of secondary alignments = 0 number of mapped bases = 152,224,141 bp number of sequenced bases = 152,174,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,435 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.91 >>>>>>> ACTG content number of A's = 42,011,404 bp (27.61%) number of C's = 30,693,920 bp (20.17%) number of T's = 43,902,523 bp (28.85%) number of G's = 35,370,453 bp (23.24%) number of N's = 196,102 bp (0.13%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,555,321 number of insertions = 12,761 mapped reads with insertion percentage = 0.55% number of deletions = 28,557 mapped reads with deletion percentage = 1.23% homopolymer indels = 42.54% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.4752X There is a 4.38% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 15082133 0.060509911427663 0.9749472143381996 chr2 243199373 14130699 0.058103352922706755 0.4784031706269205 chr3 198022430 9704402 0.04900657970917739 0.24826797937311323 chr4 191154276 6905709 0.03612636423576525 0.23191828150554822 chr5 180915260 7407594 0.040945103248891224 0.2191867536771967 chr6 171115067 7047188 0.041183912811137785 0.26268091225865975 chr7 159138663 8771310 0.055117404121963746 0.8539325800729803 chr8 146364022 7017607 0.04794625690184983 0.35333502597727084 chr9 141213431 5583068 0.03953638092682558 0.35627342222517816 chr10 135534747 11047398 0.08150971056890673 0.6489616815142395 chr11 135006516 8458072 0.062649361309346 0.40868458156511883 chr12 133851895 7123341 0.05321808107386152 0.2518748800066379 chr13 115169878 3545574 0.030785601769935018 0.1878405835388733 chr14 107349540 4160711 0.03875853590057302 0.23921840644552592 chr15 102531392 3488598 0.03402468192375658 0.21834777192576227 chr16 90354753 3666400 0.04057783213684398 0.27236647115397533 chr17 81195210 4916307 0.06054922451706203 0.2994798997150352 chr18 78077248 3888005 0.049796901140777915 0.7018005698902466 chr19 59128983 4198039 0.07099799095140871 0.697291553680413 chr20 63025520 3329333 0.05282515717442712 0.2555249200601891 chr21 48129895 1516069 0.03149952851548918 0.21757331843348743 chr22 51304566 1537036 0.029959048869061675 0.18493583633041927 chrMT 16571 88849 5.361716251282361 4.059685711796201 chrX 155270560 9228539 0.05943521424795531 0.3218220419418538 chrY 59373566 382160 0.006436534399837126 0.14942247431781677