BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432714.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 357,517,404 number of mapped reads = 357,355,505 (99.95%) number of supplementary alignments = 215,802 (0.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 178,682,663 number of mapped paired reads (second in pair) = 178,672,842 number of mapped paired reads (both in pair) = 357,295,574 number of mapped paired reads (singletons) = 59,931 number of mapped bases = 48,995,341,957 bp number of sequenced bases = 48,948,194,105 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 163,248,228 duplication rate = 30.41% >>>>>>> Insert size mean insert size = 97,293.1988 std insert size = 3,191,988.6438 median insert size = 304 >>>>>>> Mapping quality mean mapping quality = 55.3104 >>>>>>> ACTG content number of A's = 13,267,657,082 bp (27.11%) number of C's = 10,716,150,964 bp (21.89%) number of T's = 13,111,084,454 bp (26.79%) number of G's = 11,853,142,965 bp (24.22%) number of N's = 158,640 bp (0%) GC percentage = 46.11% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 445,810,221 number of insertions = 10,091,589 mapped reads with insertion percentage = 2.75% number of deletions = 31,728,366 mapped reads with deletion percentage = 8.48% homopolymer indels = 51.08% >>>>>>> Coverage mean coverageData = 15.8269X std coverageData = 47.1483X There is a 65.47% of reference with a coverageData >= 1X There is a 55.54% of reference with a coverageData >= 2X There is a 48.82% of reference with a coverageData >= 3X There is a 43.84% of reference with a coverageData >= 4X There is a 39.92% of reference with a coverageData >= 5X There is a 36.73% of reference with a coverageData >= 6X There is a 34.05% of reference with a coverageData >= 7X There is a 31.77% of reference with a coverageData >= 8X There is a 29.79% of reference with a coverageData >= 9X There is a 28.05% of reference with a coverageData >= 10X There is a 26.5% of reference with a coverageData >= 11X There is a 25.12% of reference with a coverageData >= 12X There is a 23.88% of reference with a coverageData >= 13X There is a 22.75% of reference with a coverageData >= 14X There is a 21.72% of reference with a coverageData >= 15X There is a 20.78% of reference with a coverageData >= 16X There is a 19.91% of reference with a coverageData >= 17X There is a 19.11% of reference with a coverageData >= 18X There is a 18.37% of reference with a coverageData >= 19X There is a 17.68% of reference with a coverageData >= 20X There is a 17.04% of reference with a coverageData >= 21X There is a 16.44% of reference with a coverageData >= 22X There is a 15.88% of reference with a coverageData >= 23X There is a 15.35% of reference with a coverageData >= 24X There is a 14.85% of reference with a coverageData >= 25X There is a 14.38% of reference with a coverageData >= 26X There is a 13.94% of reference with a coverageData >= 27X There is a 13.52% of reference with a coverageData >= 28X There is a 13.12% of reference with a coverageData >= 29X There is a 12.74% of reference with a coverageData >= 30X There is a 12.38% of reference with a coverageData >= 31X There is a 12.04% of reference with a coverageData >= 32X There is a 11.71% of reference with a coverageData >= 33X There is a 11.4% of reference with a coverageData >= 34X There is a 11.1% of reference with a coverageData >= 35X There is a 10.82% of reference with a coverageData >= 36X There is a 10.55% of reference with a coverageData >= 37X There is a 10.29% of reference with a coverageData >= 38X There is a 10.04% of reference with a coverageData >= 39X There is a 9.8% of reference with a coverageData >= 40X There is a 9.57% of reference with a coverageData >= 41X There is a 9.35% of reference with a coverageData >= 42X There is a 9.13% of reference with a coverageData >= 43X There is a 8.93% of reference with a coverageData >= 44X There is a 8.73% of reference with a coverageData >= 45X There is a 8.54% of reference with a coverageData >= 46X There is a 8.35% of reference with a coverageData >= 47X There is a 8.18% of reference with a coverageData >= 48X There is a 8.01% of reference with a coverageData >= 49X There is a 7.84% of reference with a coverageData >= 50X There is a 7.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4787159461 19.206208762063625 54.347286356828604 chr2 243199373 4112087463 16.908297962593842 53.19405401331791 chr3 198022430 3669063429 18.528524415138225 49.05035057660212 chr4 191154276 1893018021 9.903090114499976 31.57449188773329 chr5 180915260 2952719346 16.32100766955756 45.874224081481344 chr6 171115067 2862664367 16.72946992446901 46.54974809532446 chr7 159138663 2593089515 16.294528721785227 44.763766522061985 chr8 146364022 2538017430 17.340446069458245 50.209902959248474 chr9 141213431 2216570623 15.696599164140414 50.426443913010964 chr10 135534747 2459954229 18.149989456209337 48.27624247875155 chr11 135006516 2667105322 19.75538219207138 53.23820967776349 chr12 133851895 2268531749 16.94807345835485 46.596770714400066 chr13 115169878 1061740845 9.218910911757673 31.320195010519928 chr14 107349540 1639930362 15.276547640539494 44.60242284843678 chr15 102531392 1330851153 12.979938407546442 38.40108821463422 chr16 90354753 1269769565 14.053157391731235 49.83547946071746 chr17 81195210 1372837841 16.907867360648492 45.00763101827907 chr18 78077248 1328794056 17.01896634471543 48.57441993036441 chr19 59128983 1613689470 27.29100667941473 72.44002334356617 chr20 63025520 1496745771 23.748249455141345 58.428895660401665 chr21 48129895 605778140 12.586317505990818 46.74542916701449 chr22 51304566 927847036 18.085077183968384 53.40129348763178 chrMT 16571 7722369 466.01707802788 908.3311408449182 chrX 155270560 1177229444 7.581794282187171 22.28198893483781 chrY 59373566 142424950 2.3987939346610916 20.898942744198283