BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438297.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 = 646,428,536 number of mapped reads = 644,293,356 (99.67%) number of supplementary alignments = 10,932,484 (1.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 322,388,275 number of mapped paired reads (second in pair) = 321,905,081 number of mapped paired reads (both in pair) = 642,709,808 number of mapped paired reads (singletons) = 1,583,548 number of mapped bases = 92,999,159,666 bp number of sequenced bases = 92,970,302,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 332,330,251 duplication rate = 47.34% >>>>>>> Insert size mean insert size = 47,289.0307 std insert size = 2,129,015.5122 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 54.7017 >>>>>>> ACTG content number of A's = 27,553,826,665 bp (29.64%) number of C's = 19,091,954,250 bp (20.54%) number of T's = 26,182,854,997 bp (28.16%) number of G's = 20,140,972,194 bp (21.66%) number of N's = 694,728 bp (0%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 475,759,457 number of insertions = 12,723,053 mapped reads with insertion percentage = 1.94% number of deletions = 11,439,156 mapped reads with deletion percentage = 1.74% homopolymer indels = 49.15% >>>>>>> Coverage mean coverageData = 30.0415X std coverageData = 144.2087X There is a 68.29% of reference with a coverageData >= 1X There is a 66.66% of reference with a coverageData >= 2X There is a 65.25% of reference with a coverageData >= 3X There is a 64.1% of reference with a coverageData >= 4X There is a 62.96% of reference with a coverageData >= 5X There is a 61.89% of reference with a coverageData >= 6X There is a 60.8% of reference with a coverageData >= 7X There is a 59.73% of reference with a coverageData >= 8X There is a 58.63% of reference with a coverageData >= 9X There is a 57.53% of reference with a coverageData >= 10X There is a 56.41% of reference with a coverageData >= 11X There is a 55.28% of reference with a coverageData >= 12X There is a 54.14% of reference with a coverageData >= 13X There is a 52.99% of reference with a coverageData >= 14X There is a 51.83% of reference with a coverageData >= 15X There is a 50.68% of reference with a coverageData >= 16X There is a 49.52% of reference with a coverageData >= 17X There is a 48.36% of reference with a coverageData >= 18X There is a 47.21% of reference with a coverageData >= 19X There is a 46.07% of reference with a coverageData >= 20X There is a 44.94% of reference with a coverageData >= 21X There is a 43.83% of reference with a coverageData >= 22X There is a 42.72% of reference with a coverageData >= 23X There is a 41.64% of reference with a coverageData >= 24X There is a 40.57% of reference with a coverageData >= 25X There is a 39.52% of reference with a coverageData >= 26X There is a 38.49% of reference with a coverageData >= 27X There is a 37.48% of reference with a coverageData >= 28X There is a 36.49% of reference with a coverageData >= 29X There is a 35.53% of reference with a coverageData >= 30X There is a 34.59% of reference with a coverageData >= 31X There is a 33.67% of reference with a coverageData >= 32X There is a 32.77% of reference with a coverageData >= 33X There is a 31.9% of reference with a coverageData >= 34X There is a 31.05% of reference with a coverageData >= 35X There is a 30.22% of reference with a coverageData >= 36X There is a 29.41% of reference with a coverageData >= 37X There is a 28.62% of reference with a coverageData >= 38X There is a 27.86% of reference with a coverageData >= 39X There is a 27.11% of reference with a coverageData >= 40X There is a 26.39% of reference with a coverageData >= 41X There is a 25.69% of reference with a coverageData >= 42X There is a 25.01% of reference with a coverageData >= 43X There is a 24.34% of reference with a coverageData >= 44X There is a 23.7% of reference with a coverageData >= 45X There is a 23.07% of reference with a coverageData >= 46X There is a 22.47% of reference with a coverageData >= 47X There is a 21.88% of reference with a coverageData >= 48X There is a 21.31% of reference with a coverageData >= 49X There is a 20.75% of reference with a coverageData >= 50X There is a 20.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9033498481 36.24263179268067 50.83014566689934 chr2 243199373 7483838586 30.772441942109776 103.9016650076485 chr3 198022430 7438847280 37.565680211075076 102.62212783529242 chr4 191154276 5549390846 29.030953228584853 35.71890206649472 chr5 180915260 5215354412 28.827609191176023 37.14739321548288 chr6 171115067 5314184819 31.0562062836933 41.05862520698786 chr7 159138663 4871201834 30.609794893149253 41.33068703214534 chr8 146364022 4288843406 29.30257960525299 37.626548114900054 chr9 141213431 4020480130 28.470947143830816 40.81832825666815 chr10 135534747 3816129734 28.15609884895421 42.87350704565508 chr11 135006516 3057200139 22.64483396490285 38.565589107791624 chr12 133851895 4246800775 31.727610393562227 44.96832576315817 chr13 115169878 2693696875 23.388901002395784 37.35666828489699 chr14 107349540 3012187898 28.05962557454834 44.247938503968456 chr15 102531392 3538499372 34.51137552097215 47.45595503066645 chr16 90354753 1909262381 21.130735435688702 55.21344166570464 chr17 81195210 3663000153 45.11350057472602 60.45552112900244 chr18 78077248 1886622725 24.163540254390114 34.1167746636408 chr19 59128983 2228545643 37.689564912692646 122.13396706451556 chr20 63025520 2740648411 43.48474095890046 52.17956145472697 chr21 48129895 1314489190 27.311283143252233 59.686194609972894 chr22 51304566 1580131791 30.799048002861966 48.91654398926925 chrMT 16571 877029361 52925.55434192264 21314.622223872506 chrX 155270560 3087379396 19.883868493808485 30.51599805004401 chrY 59373566 131896028 2.2214604391455954 18.938742664061223