BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237819.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 = 4,112,196 number of mapped reads = 3,951,867 (96.1%) number of supplementary alignments = 34,816 (0.85%) number of secondary alignments = 0 number of mapped bases = 290,322,703 bp number of sequenced bases = 290,159,379 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 262,402 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2063 >>>>>>> ACTG content number of A's = 88,903,144 bp (30.64%) number of C's = 56,220,441 bp (19.38%) number of T's = 88,507,916 bp (30.5%) number of G's = 56,016,358 bp (19.31%) number of N's = 511,520 bp (0.18%) GC percentage = 38.68% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 2,548,440 number of insertions = 23,229 mapped reads with insertion percentage = 0.58% number of deletions = 89,769 mapped reads with deletion percentage = 2.24% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.0938X std coverageData = 1.2424X There is a 3.72% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 1.19% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 34418994 0.13808990269276 2.6382418072680665 chr2 243199373 16931966 0.06962175021725898 0.8471352790957157 chr3 198022430 6891798 0.034803118010419326 0.4111969863518231 chr4 191154276 11714090 0.06128081592064412 0.6531639825441965 chr5 180915260 5804911 0.03208635357791267 0.3796509983162013 chr6 171115067 17387251 0.10161145540737217 0.7270954793688255 chr7 159138663 29866436 0.18767554934151987 2.4304817964327343 chr8 146364022 23428018 0.16006678198553467 1.2807058720917857 chr9 141213431 12529169 0.08872505193928756 0.881573910859822 chr10 135534747 33929485 0.25033790781341114 1.7286173325635132 chr11 135006516 27035616 0.20025415662159596 1.4933410453441183 chr12 133851895 12896725 0.09635070911771551 0.6484164118832664 chr13 115169878 2521571 0.021894361996285173 0.2950058714994445 chr14 107349540 2381742 0.02218679278923785 0.367093122883896 chr15 102531392 3794465 0.03700783658530648 0.39084093281212706 chr16 90354753 7587298 0.0839723174275071 0.6964721383773331 chr17 81195210 5574326 0.06865338484868751 0.7242865098684869 chr18 78077248 2505107 0.032084980761617005 1.412606854090448 chr19 59128983 3457099 0.05846708034873524 1.4221601481535278 chr20 63025520 5540771 0.08791313423514792 0.6324983555391173 chr21 48129895 4707971 0.09781801934120156 0.7461482760622137 chr22 51304566 1614518 0.03146928481960066 0.34377325658895014 chrMT 16571 342666 20.678655482469374 15.245138652225075 chrX 155270560 16655692 0.10726883447834541 0.7629158451364948 chrY 59373566 805018 0.013558525354532351 0.45240203587161776