BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081926.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 = 2,731,989 number of mapped reads = 2,510,299 (91.89%) number of supplementary alignments = 16,037 (0.59%) number of secondary alignments = 0 number of mapped bases = 170,367,279 bp number of sequenced bases = 170,303,793 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,923 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6334 >>>>>>> ACTG content number of A's = 48,200,912 bp (28.3%) number of C's = 31,225,383 bp (18.34%) number of T's = 54,158,218 bp (31.8%) number of G's = 36,697,696 bp (21.55%) number of N's = 21,584 bp (0.01%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,265,485 number of insertions = 11,880 mapped reads with insertion percentage = 0.47% number of deletions = 35,711 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.25% >>>>>>> Coverage mean coverageData = 0.055X std coverageData = 0.3968X There is a 4.67% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.1% 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% 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 15474628 0.06208461161667477 0.5527290964364932 chr2 243199373 14847995 0.06105276842140543 0.5591812122781349 chr3 198022430 11195542 0.056536736772697924 0.27173285236895683 chr4 191154276 8867167 0.04638748965259872 0.2578935007040062 chr5 180915260 9707736 0.05365902246167625 0.26453631174596864 chr6 171115067 14984012 0.08756687685485931 0.4146322137620511 chr7 159138663 11505334 0.07229754091876467 0.46622866282690145 chr8 146364022 9837581 0.06721310924347242 0.5884329341138137 chr9 141213431 9290486 0.06579038505197143 0.46163640914845155 chr10 135534747 6455242 0.04762794886834444 0.4011104339015582 chr11 135006516 7449191 0.055176529405439954 0.31766005388394647 chr12 133851895 7054204 0.052701562424648525 0.27076437854849483 chr13 115169878 4489995 0.03898584489253345 0.22474637201028586 chr14 107349540 4228770 0.03939253023347841 0.2539835235737157 chr15 102531392 3839179 0.03744393716999375 0.2193404329895311 chr16 90354753 3681654 0.0407466555743891 0.26263202172160277 chr17 81195210 3948499 0.04862970364877436 0.26761490157489043 chr18 78077248 5181060 0.06635812778647117 0.6677322634203631 chr19 59128983 2271164 0.03841033423490473 0.4979756662928598 chr20 63025520 4349979 0.06901932740896069 0.3045042323765063 chr21 48129895 1851979 0.03847876667921258 0.25148695043082137 chr22 51304566 1385152 0.026998610610993182 0.18424194902172059 chrMT 16571 2830 0.1707802788003138 0.43825101912694103 chrX 155270560 8108528 0.05222192796883066 0.29640416695595395 chrY 59373566 359372 0.0060527272355512555 0.12801580122932285