BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174024.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 = 5,438,072 number of mapped reads = 5,297,882 (97.42%) number of supplementary alignments = 529,639 (9.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,651,805 number of mapped paired reads (second in pair) = 2,646,077 number of mapped paired reads (both in pair) = 5,204,848 number of mapped paired reads (singletons) = 93,034 number of mapped bases = 625,318,644 bp number of sequenced bases = 624,933,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,118,041 duplication rate = 65.7% >>>>>>> Insert size mean insert size = 760,498.168 std insert size = 8,130,163.5262 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 52.8014 >>>>>>> ACTG content number of A's = 187,686,448 bp (30.03%) number of C's = 122,313,660 bp (19.57%) number of T's = 187,319,361 bp (29.97%) number of G's = 127,606,301 bp (20.42%) number of N's = 7,745 bp (0%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 6,392,743 number of insertions = 64,285 mapped reads with insertion percentage = 1.17% number of deletions = 163,917 mapped reads with deletion percentage = 3.02% homopolymer indels = 42.03% >>>>>>> Coverage mean coverageData = 0.202X std coverageData = 2.9576X There is a 4.21% of reference with a coverageData >= 1X There is a 3.35% of reference with a coverageData >= 2X There is a 2.59% of reference with a coverageData >= 3X There is a 2.13% of reference with a coverageData >= 4X There is a 1.61% of reference with a coverageData >= 5X There is a 1.3% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.78% of reference with a coverageData >= 8X There is a 0.57% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 47408753 0.19020515499538113 1.9760806549795993 chr2 243199373 57537926 0.23658747672840422 9.024794160553714 chr3 198022430 48002723 0.24241053399859805 1.4421297672549915 chr4 191154276 32042533 0.16762655625867348 1.3807716553883773 chr5 180915260 39797705 0.21997981264819783 1.3450348622500363 chr6 171115067 35009415 0.20459574725818855 1.4709570860936825 chr7 159138663 36292018 0.2280528019768521 1.8926544179727613 chr8 146364022 31209422 0.21323151395771292 1.8053096606856645 chr9 141213431 27507424 0.19479325589079413 1.5370523716331757 chr10 135534747 27821152 0.20526951660595197 2.3585907280844163 chr11 135006516 23013191 0.17045985395253072 1.2207964759911458 chr12 133851895 28684437 0.21429981996145814 1.3423025235093033 chr13 115169878 15440744 0.13406929197233325 1.0566999442420806 chr14 107349540 19372410 0.18046104342878413 1.2213802058306358 chr15 102531392 18395436 0.17941272074020023 1.2360490495625442 chr16 90354753 20315758 0.22484437537004834 1.6409615991123945 chr17 81195210 26303902 0.32395879017986406 1.8024964881521464 chr18 78077248 11083331 0.14195340235352558 2.3839220193368944 chr19 59128983 10404340 0.17596007020787083 1.5970789368864458 chr20 63025520 28402193 0.450645912957164 2.133921275119566 chr21 48129895 8224738 0.1708862651788457 1.2319646326523275 chr22 51304566 5348304 0.10424616007861756 0.8878279145592306 chrMT 16571 631247 38.09347655542816 32.802491732590425 chrX 155270560 25979200 0.16731568431259602 1.1802470600072796 chrY 59373566 1090342 0.018364098258811 0.7351744258273775