BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174059.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,686,314 number of mapped reads = 3,577,050 (97.04%) number of supplementary alignments = 369,804 (10.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,794,471 number of mapped paired reads (second in pair) = 1,782,579 number of mapped paired reads (both in pair) = 3,502,842 number of mapped paired reads (singletons) = 74,208 number of mapped bases = 420,482,410 bp number of sequenced bases = 420,223,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,804,077 duplication rate = 64.35% >>>>>>> Insert size mean insert size = 964,593.3625 std insert size = 9,157,144.1275 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.5432 >>>>>>> ACTG content number of A's = 126,047,889 bp (30%) number of C's = 82,740,696 bp (19.69%) number of T's = 125,715,175 bp (29.92%) number of G's = 85,714,641 bp (20.4%) number of N's = 5,433 bp (0%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 4,503,314 number of insertions = 47,288 mapped reads with insertion percentage = 1.27% number of deletions = 102,242 mapped reads with deletion percentage = 2.78% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.1358X std coverageData = 2.155X There is a 2.78% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 1.7% of reference with a coverageData >= 3X There is a 1.41% of reference with a coverageData >= 4X There is a 1.09% of reference with a coverageData >= 5X There is a 0.89% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 37526648 0.15055789168926484 1.590966538012093 chr2 243199373 37691247 0.154980855974493 6.001271808240224 chr3 198022430 33853620 0.17095851212410634 1.2171211977328473 chr4 191154276 27417755 0.14343260100548313 1.4739737240592348 chr5 180915260 27059629 0.14957073825613162 1.1373416996291374 chr6 171115067 25349017 0.14814018101632162 1.160748270383795 chr7 159138663 30657974 0.19264943805642 2.109492476606798 chr8 146364022 13399048 0.09154604947929075 1.0486489990383165 chr9 141213431 18063935 0.12791938324903387 1.1738205801186892 chr10 135534747 17974493 0.13261907664165265 2.5803876942447825 chr11 135006516 18617954 0.13790411419845838 1.0971860501736492 chr12 133851895 16391080 0.12245683932976817 1.0189503980803787 chr13 115169878 8697881 0.07552218645225968 0.8068276945266549 chr14 107349540 10374736 0.09664443834598639 0.922752199642912 chr15 102531392 14550292 0.14191060626583515 1.0940065206339014 chr16 90354753 18435605 0.2040358076126886 1.873967003212027 chr17 81195210 10549089 0.1299225533131819 1.153440070071612 chr18 78077248 6403225 0.08201140747173875 1.5406647659017707 chr19 59128983 8069827 0.136478366286124 1.6474154510330015 chr20 63025520 12682833 0.2012332940688153 1.337666494591133 chr21 48129895 6491466 0.1348738865937688 1.1759052479131835 chr22 51304566 3954564 0.07708015695912913 0.766394165626206 chrMT 16571 1062338 64.10826142055399 50.817370347988906 chrX 155270560 14440837 0.09300434673514413 0.8904602673677056 chrY 59373566 767317 0.012923545808247394 0.7966764182075394