BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716533.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,417,079 number of mapped reads = 2,268,559 (93.86%) number of supplementary alignments = 45,784 (1.89%) number of secondary alignments = 0 number of mapped bases = 175,079,506 bp number of sequenced bases = 175,014,275 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,713 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.447 >>>>>>> ACTG content number of A's = 41,847,314 bp (23.91%) number of C's = 36,337,141 bp (20.76%) number of T's = 53,723,700 bp (30.7%) number of G's = 43,100,077 bp (24.63%) number of N's = 6,043 bp (0%) GC percentage = 45.39% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,141,514 number of insertions = 15,281 mapped reads with insertion percentage = 0.66% number of deletions = 31,679 mapped reads with deletion percentage = 1.37% homopolymer indels = 38.85% >>>>>>> Coverage mean coverageData = 0.0566X std coverageData = 0.4585X There is a 4.44% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% 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 19902599 0.07984974689391044 0.9464595140693538 chr2 243199373 12091475 0.049718364199894546 0.4256368802718251 chr3 198022430 11437724 0.05775973964161535 0.2960926914412246 chr4 191154276 8562672 0.044794561645066205 0.36668321659532754 chr5 180915260 10578416 0.05847166236833753 0.30345396883531733 chr6 171115067 11850185 0.0692527268799772 0.34798527809416685 chr7 159138663 11380100 0.07151059199234318 0.6127206384535665 chr8 146364022 11223088 0.07667928119657712 0.47482362043548665 chr9 141213431 5391614 0.03818060337334343 0.30595646519881986 chr10 135534747 7085640 0.0522791399020356 0.5596198821714143 chr11 135006516 7684597 0.056920193392739654 0.36474246241638286 chr12 133851895 6425345 0.0480033921073736 0.26845376964178624 chr13 115169878 3440743 0.029875372447646424 0.20836664638133962 chr14 107349540 3419708 0.031855823508885085 0.23974374392102604 chr15 102531392 3402004 0.0331801210696525 0.21992124947758115 chr16 90354753 6607398 0.07312728750417812 0.36159864430255373 chr17 81195210 3436886 0.042328679241053754 0.285441058373909 chr18 78077248 5253661 0.06728798894141351 0.4870136889998499 chr19 59128983 4436040 0.0750231066886437 0.6882620680199982 chr20 63025520 3978683 0.06312812651129257 0.33215448416100074 chr21 48129895 2728862 0.05669785899179709 0.35919891449298824 chr22 51304566 2826722 0.05509688942695666 0.3003768876069106 chrMT 16571 142614 8.60623981654698 7.006008522567099 chrX 155270560 11230207 0.0723266986349505 0.349446257854604 chrY 59373566 562523 0.009474300398261408 0.3267690366724047