BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230365.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 = 2,182,883 number of mapped reads = 2,039,500 (93.43%) number of supplementary alignments = 15,427 (0.71%) number of secondary alignments = 0 number of mapped bases = 146,306,683 bp number of sequenced bases = 146,227,735 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,327 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9146 >>>>>>> ACTG content number of A's = 43,789,037 bp (29.95%) number of C's = 29,271,939 bp (20.02%) number of T's = 42,912,173 bp (29.35%) number of G's = 30,173,715 bp (20.63%) number of N's = 80,871 bp (0.06%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,359,170 number of insertions = 13,153 mapped reads with insertion percentage = 0.64% number of deletions = 45,813 mapped reads with deletion percentage = 2.22% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.0473X std coverageData = 0.5756X There is a 3.85% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.12% 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 12895518 0.05173715494975637 1.525835522714839 chr2 243199373 11780971 0.0484416174872293 0.4590919452000012 chr3 198022430 8537886 0.04311575208929615 0.25715705211923096 chr4 191154276 12920723 0.06759316752087723 0.3341546235184024 chr5 180915260 6750105 0.03731086587167937 0.22917224288046675 chr6 171115067 10485016 0.061274650934157654 0.35912852656325145 chr7 159138663 6986722 0.043903359927059335 0.542073268010103 chr8 146364022 5171312 0.03533185224986506 0.35377856395434837 chr9 141213431 5600586 0.03966043428262854 0.4182196269295353 chr10 135534747 9272383 0.06841332724810413 0.5931977078489696 chr11 135006516 5853716 0.043358766476130677 0.3818104962157401 chr12 133851895 7010306 0.0523736029288192 0.2761923776244574 chr13 115169878 3527299 0.030626923126548765 0.20225107433124684 chr14 107349540 6017535 0.05605552664687711 0.29852287744719025 chr15 102531392 2815841 0.027463208536172023 0.19062526242822317 chr16 90354753 3117813 0.03450635297514454 0.28755729806606156 chr17 81195210 3536500 0.04355552501188186 0.2653563696224816 chr18 78077248 3214857 0.041175337020075295 0.8779675831294612 chr19 59128983 3911131 0.0661457512299848 0.7806174791219687 chr20 63025520 2181021 0.03460536303389484 0.23288568760872508 chr21 48129895 2083155 0.04328193527120722 0.27368383787613404 chr22 51304566 1615368 0.031485852545755866 0.20616080379909668 chrMT 16571 642 0.038742381268481084 0.21233567678808665 chrX 155270560 10554099 0.06797231233016741 0.36843481549829693 chrY 59373566 466178 0.007851608576112811 0.20124418181516956