BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438260.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 1,521,325,884 number of mapped reads = 1,510,180,186 (99.27%) number of supplementary alignments = 45,952,591 (3.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 755,412,933 number of mapped paired reads (second in pair) = 754,767,253 number of mapped paired reads (both in pair) = 1,507,042,962 number of mapped paired reads (singletons) = 3,137,224 number of mapped bases = 165,975,263,228 bp number of sequenced bases = 165,927,999,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 875,948,222 duplication rate = 52.78% >>>>>>> Insert size mean insert size = 122,709.6806 std insert size = 3,546,286.5364 median insert size = 121 >>>>>>> Mapping quality mean mapping quality = 52.0734 >>>>>>> ACTG content number of A's = 50,658,987,343 bp (30.53%) number of C's = 32,656,061,858 bp (19.68%) number of T's = 49,481,411,024 bp (29.82%) number of G's = 33,131,081,510 bp (19.97%) number of N's = 457,858 bp (0%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 575,892,599 number of insertions = 25,268,830 mapped reads with insertion percentage = 1.64% number of deletions = 18,133,119 mapped reads with deletion percentage = 1.18% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 53.6149X std coverageData = 502.6955X There is a 78.89% of reference with a coverageData >= 1X There is a 75.97% of reference with a coverageData >= 2X There is a 71.48% of reference with a coverageData >= 3X There is a 68.84% of reference with a coverageData >= 4X There is a 65.99% of reference with a coverageData >= 5X There is a 63.83% of reference with a coverageData >= 6X There is a 61.74% of reference with a coverageData >= 7X There is a 59.97% of reference with a coverageData >= 8X There is a 58.32% of reference with a coverageData >= 9X There is a 56.84% of reference with a coverageData >= 10X There is a 55.47% of reference with a coverageData >= 11X There is a 54.21% of reference with a coverageData >= 12X There is a 53.03% of reference with a coverageData >= 13X There is a 51.93% of reference with a coverageData >= 14X There is a 50.88% of reference with a coverageData >= 15X There is a 49.9% of reference with a coverageData >= 16X There is a 48.96% of reference with a coverageData >= 17X There is a 48.06% of reference with a coverageData >= 18X There is a 47.2% of reference with a coverageData >= 19X There is a 46.37% of reference with a coverageData >= 20X There is a 45.57% of reference with a coverageData >= 21X There is a 44.8% of reference with a coverageData >= 22X There is a 44.06% of reference with a coverageData >= 23X There is a 43.34% of reference with a coverageData >= 24X There is a 42.64% of reference with a coverageData >= 25X There is a 41.96% of reference with a coverageData >= 26X There is a 41.3% of reference with a coverageData >= 27X There is a 40.66% of reference with a coverageData >= 28X There is a 40.03% of reference with a coverageData >= 29X There is a 39.42% of reference with a coverageData >= 30X There is a 38.83% of reference with a coverageData >= 31X There is a 38.25% of reference with a coverageData >= 32X There is a 37.68% of reference with a coverageData >= 33X There is a 37.12% of reference with a coverageData >= 34X There is a 36.58% of reference with a coverageData >= 35X There is a 36.05% of reference with a coverageData >= 36X There is a 35.53% of reference with a coverageData >= 37X There is a 35.02% of reference with a coverageData >= 38X There is a 34.52% of reference with a coverageData >= 39X There is a 34.03% of reference with a coverageData >= 40X There is a 33.55% of reference with a coverageData >= 41X There is a 33.08% of reference with a coverageData >= 42X There is a 32.62% of reference with a coverageData >= 43X There is a 32.17% of reference with a coverageData >= 44X There is a 31.73% of reference with a coverageData >= 45X There is a 31.3% of reference with a coverageData >= 46X There is a 30.87% of reference with a coverageData >= 47X There is a 30.45% of reference with a coverageData >= 48X There is a 30.04% of reference with a coverageData >= 49X There is a 29.64% of reference with a coverageData >= 50X There is a 29.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9994957715 40.10003134555881 86.06531739257414 chr2 243199373 18118062038 74.49880242084342 1759.850242939038 chr3 198022430 15860587642 80.09490461257343 123.9930157853045 chr4 191154276 9907696333 51.83089042172407 93.38974516812155 chr5 180915260 9336634201 51.60777593332923 98.44140762494206 chr6 171115067 11602152342 67.80321888311565 118.73407796998686 chr7 159138663 9446099527 59.35766550332272 104.31844947249562 chr8 146364022 13080884185 89.37226516636719 124.47322863043574 chr9 141213431 4128407071 29.235229551217405 76.93027004056016 chr10 135534747 7884873047 58.176026602240974 103.72213599420144 chr11 135006516 6780409699 50.222832940893014 89.89103358576024 chr12 133851895 5938803983 44.368471458696945 93.82682094369382 chr13 115169878 6977296025 60.58264666217672 102.85489210435777 chr14 107349540 2335702821 21.757921095889184 59.20294594988546 chr15 102531392 4657209860 45.42228257273636 93.99454225272241 chr16 90354753 3149800620 34.860375524461894 73.44068559511317 chr17 81195210 2324135368 28.624045285430014 62.87959038754613 chr18 78077248 3588905517 45.96608626625775 85.16044139882978 chr19 59128983 929650700 15.722419917149598 40.38996079050744 chr20 63025520 1486602675 23.587313123318935 62.6126694912806 chr21 48129895 2664129207 55.35289879606012 102.85873853925897 chr22 51304566 732072047 14.269140235978217 44.8265723172502 chrMT 16571 340481 20.546798624102347 15.828354102112435 chrX 155270560 14860411232 95.70656041943818 149.1654902733573 chrY 59373566 189438892 3.190626818675503 25.622438014584265