BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432715.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 = 393,256,278 number of mapped reads = 393,066,363 (99.95%) number of supplementary alignments = 230,363 (0.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 196,539,420 number of mapped paired reads (second in pair) = 196,526,943 number of mapped paired reads (both in pair) = 392,997,274 number of mapped paired reads (singletons) = 69,089 number of mapped bases = 53,877,454,844 bp number of sequenced bases = 53,825,580,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,556,028 duplication rate = 31.28% >>>>>>> Insert size mean insert size = 72,916.2599 std insert size = 2,717,594.9664 median insert size = 286 >>>>>>> Mapping quality mean mapping quality = 55.4117 >>>>>>> ACTG content number of A's = 14,687,234,780 bp (27.29%) number of C's = 11,704,217,024 bp (21.74%) number of T's = 14,520,619,241 bp (26.98%) number of G's = 12,909,811,485 bp (23.98%) number of N's = 3,698,051 bp (0.01%) GC percentage = 45.73% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 524,991,478 number of insertions = 11,204,178 mapped reads with insertion percentage = 2.78% number of deletions = 35,142,517 mapped reads with deletion percentage = 8.54% homopolymer indels = 51.41% >>>>>>> Coverage mean coverageData = 17.404X std coverageData = 50.3999X There is a 66.16% of reference with a coverageData >= 1X There is a 56.87% of reference with a coverageData >= 2X There is a 50.45% of reference with a coverageData >= 3X There is a 45.63% of reference with a coverageData >= 4X There is a 41.8% of reference with a coverageData >= 5X There is a 38.65% of reference with a coverageData >= 6X There is a 35.98% of reference with a coverageData >= 7X There is a 33.69% of reference with a coverageData >= 8X There is a 31.69% of reference with a coverageData >= 9X There is a 29.92% of reference with a coverageData >= 10X There is a 28.35% of reference with a coverageData >= 11X There is a 26.94% of reference with a coverageData >= 12X There is a 25.67% of reference with a coverageData >= 13X There is a 24.51% of reference with a coverageData >= 14X There is a 23.44% of reference with a coverageData >= 15X There is a 22.47% of reference with a coverageData >= 16X There is a 21.57% of reference with a coverageData >= 17X There is a 20.74% of reference with a coverageData >= 18X There is a 19.96% of reference with a coverageData >= 19X There is a 19.24% of reference with a coverageData >= 20X There is a 18.57% of reference with a coverageData >= 21X There is a 17.93% of reference with a coverageData >= 22X There is a 17.34% of reference with a coverageData >= 23X There is a 16.78% of reference with a coverageData >= 24X There is a 16.26% of reference with a coverageData >= 25X There is a 15.76% of reference with a coverageData >= 26X There is a 15.29% of reference with a coverageData >= 27X There is a 14.84% of reference with a coverageData >= 28X There is a 14.42% of reference with a coverageData >= 29X There is a 14.02% of reference with a coverageData >= 30X There is a 13.63% of reference with a coverageData >= 31X There is a 13.27% of reference with a coverageData >= 32X There is a 12.92% of reference with a coverageData >= 33X There is a 12.59% of reference with a coverageData >= 34X There is a 12.27% of reference with a coverageData >= 35X There is a 11.97% of reference with a coverageData >= 36X There is a 11.67% of reference with a coverageData >= 37X There is a 11.39% of reference with a coverageData >= 38X There is a 11.12% of reference with a coverageData >= 39X There is a 10.87% of reference with a coverageData >= 40X There is a 10.62% of reference with a coverageData >= 41X There is a 10.38% of reference with a coverageData >= 42X There is a 10.15% of reference with a coverageData >= 43X There is a 9.92% of reference with a coverageData >= 44X There is a 9.71% of reference with a coverageData >= 45X There is a 9.5% of reference with a coverageData >= 46X There is a 9.3% of reference with a coverageData >= 47X There is a 9.11% of reference with a coverageData >= 48X There is a 8.92% of reference with a coverageData >= 49X There is a 8.74% of reference with a coverageData >= 50X There is a 8.57% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4830145544 19.378670049532193 54.407975422908216 chr2 243199373 3780433068 15.544583941012052 51.22901266730635 chr3 198022430 3303183472 16.68085515363083 43.66186316773655 chr4 191154276 2566466256 13.42615142964419 38.96339617410894 chr5 180915260 2900799221 16.034021790091117 43.89528547590675 chr6 171115067 2702179954 15.791595686895299 43.947199323882614 chr7 159138663 3469563236 21.802138905741593 57.00007528599795 chr8 146364022 4547117837 31.067182869571596 77.63315088265921 chr9 141213431 2219329157 15.716133665784241 50.75565093293154 chr10 135534747 2579778467 19.034074465052125 49.60846374134912 chr11 135006516 2671870586 19.790678740276505 50.97005909330281 chr12 133851895 2443606969 18.256050607277544 49.35595839350114 chr13 115169878 1370339551 11.898419749997478 36.85669674094918 chr14 107349540 1734585167 16.158291567900523 46.313785187096805 chr15 102531392 1668040856 16.26858685386813 46.460858285176585 chr16 90354753 1722508011 19.063833985579045 59.4153864391053 chr17 81195210 1888145158 23.25439096715188 58.59911148079428 chr18 78077248 1397580754 17.899974573898916 50.24125083900996 chr19 59128983 1371230832 23.190502566228815 61.41235036503101 chr20 63025520 1576435659 25.01265612723227 60.134171622988326 chr21 48129895 673473962 13.99284087363997 51.567922016228 chr22 51304566 1085590609 21.159726972449196 60.481694859552576 chrMT 16571 6366372 384.187556574739 724.6959120770855 chrX 155270560 1206800199 7.772240912894241 22.42142987940661 chrY 59373566 161883947 2.726532325850194 22.608733107623678