BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237278.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,647,657 number of mapped reads = 2,258,852 (85.32%) number of supplementary alignments = 15,882 (0.6%) number of secondary alignments = 0 number of mapped bases = 154,430,445 bp number of sequenced bases = 154,345,002 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,104 duplication rate = 4.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3833 >>>>>>> ACTG content number of A's = 44,878,638 bp (29.08%) number of C's = 28,444,621 bp (18.43%) number of T's = 48,677,250 bp (31.54%) number of G's = 32,341,831 bp (20.95%) number of N's = 2,662 bp (0%) GC percentage = 39.38% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,257,590 number of insertions = 13,757 mapped reads with insertion percentage = 0.6% number of deletions = 47,806 mapped reads with deletion percentage = 2.09% homopolymer indels = 45.37% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.5329X There is a 3.45% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14171789 0.05685758752833759 0.8469882461237218 chr2 243199373 11026275 0.04533841869732123 0.6466166624520818 chr3 198022430 13567842 0.06851669278071176 0.35299607208794775 chr4 191154276 3825808 0.020014242318074013 0.391645500316479 chr5 180915260 7451546 0.04118804571819978 0.28759153889090167 chr6 171115067 23002448 0.13442678311898743 0.7994640574896258 chr7 159138663 5925657 0.03723580987984045 0.49411820970168424 chr8 146364022 12217730 0.08347495397468649 0.5731832175936846 chr9 141213431 6889982 0.048791265471058484 0.5959439690872145 chr10 135534747 2005176 0.014794553015987848 0.5677649087059612 chr11 135006516 5974276 0.04425176041132711 0.37358494448300344 chr12 133851895 3366369 0.025149953984588712 0.23565912127971192 chr13 115169878 4961722 0.043081768307508324 0.280983501165147 chr14 107349540 7184518 0.06692639763523905 0.3893930512276834 chr15 102531392 4360245 0.04252595146664936 0.2757926153096002 chr16 90354753 1793820 0.019853078453991237 0.3043389597162113 chr17 81195210 5702082 0.0702268274199919 0.4549872497733957 chr18 78077248 2681878 0.034349033408554566 1.0983730891615973 chr19 59128983 3445261 0.05826687396263859 0.4737547660821806 chr20 63025520 3863761 0.06130470641099034 0.35090658489690335 chr21 48129895 2240288 0.046546704496238774 0.4302241930127214 chr22 51304566 764638 0.014903897637492928 0.1573713984086479 chrMT 16571 109360 6.59948102106089 4.867163773917338 chrX 155270560 7417039 0.04776848231886328 0.329779724825608 chrY 59373566 480935 0.008100153526234216 0.39159398506411963