BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365346.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 535,286,226 number of mapped reads = 509,738,309 (95.23%) number of supplementary alignments = 2,238,897 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 255,340,514 number of mapped paired reads (second in pair) = 254,397,795 number of mapped paired reads (both in pair) = 506,826,152 number of mapped paired reads (singletons) = 2,912,157 number of mapped bases = 51,805,324,814 bp number of sequenced bases = 51,788,088,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 357,759,498 duplication rate = 43.01% >>>>>>> Insert size mean insert size = 80,711.7955 std insert size = 2,760,225.9072 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 53.7527 >>>>>>> ACTG content number of A's = 15,516,523,661 bp (29.96%) number of C's = 10,130,201,690 bp (19.56%) number of T's = 15,015,862,678 bp (28.99%) number of G's = 11,104,943,532 bp (21.44%) number of N's = 20,556,661 bp (0.04%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 300,592,188 number of insertions = 15,731,460 mapped reads with insertion percentage = 3.02% number of deletions = 8,194,453 mapped reads with deletion percentage = 1.57% homopolymer indels = 50.02% >>>>>>> Coverage mean coverageData = 16.7346X std coverageData = 137.5103X There is a 86.12% of reference with a coverageData >= 1X There is a 82.25% of reference with a coverageData >= 2X There is a 78.23% of reference with a coverageData >= 3X There is a 74.8% of reference with a coverageData >= 4X There is a 71.2% of reference with a coverageData >= 5X There is a 67.96% of reference with a coverageData >= 6X There is a 64.6% of reference with a coverageData >= 7X There is a 61.51% of reference with a coverageData >= 8X There is a 58.34% of reference with a coverageData >= 9X There is a 55.41% of reference with a coverageData >= 10X There is a 52.43% of reference with a coverageData >= 11X There is a 49.66% of reference with a coverageData >= 12X There is a 46.9% of reference with a coverageData >= 13X There is a 44.32% of reference with a coverageData >= 14X There is a 41.77% of reference with a coverageData >= 15X There is a 39.39% of reference with a coverageData >= 16X There is a 37.07% of reference with a coverageData >= 17X There is a 34.9% of reference with a coverageData >= 18X There is a 32.8% of reference with a coverageData >= 19X There is a 30.86% of reference with a coverageData >= 20X There is a 28.98% of reference with a coverageData >= 21X There is a 27.23% of reference with a coverageData >= 22X There is a 25.56% of reference with a coverageData >= 23X There is a 24.01% of reference with a coverageData >= 24X There is a 22.53% of reference with a coverageData >= 25X There is a 21.16% of reference with a coverageData >= 26X There is a 19.85% of reference with a coverageData >= 27X There is a 18.64% of reference with a coverageData >= 28X There is a 17.49% of reference with a coverageData >= 29X There is a 16.42% of reference with a coverageData >= 30X There is a 15.41% of reference with a coverageData >= 31X There is a 14.48% of reference with a coverageData >= 32X There is a 13.59% of reference with a coverageData >= 33X There is a 12.77% of reference with a coverageData >= 34X There is a 11.99% of reference with a coverageData >= 35X There is a 11.27% of reference with a coverageData >= 36X There is a 10.59% of reference with a coverageData >= 37X There is a 9.96% of reference with a coverageData >= 38X There is a 9.37% of reference with a coverageData >= 39X There is a 8.82% of reference with a coverageData >= 40X There is a 8.3% of reference with a coverageData >= 41X There is a 7.82% of reference with a coverageData >= 42X There is a 7.36% of reference with a coverageData >= 43X There is a 6.94% of reference with a coverageData >= 44X There is a 6.54% of reference with a coverageData >= 45X There is a 6.17% of reference with a coverageData >= 46X There is a 5.82% of reference with a coverageData >= 47X There is a 5.5% of reference with a coverageData >= 48X There is a 5.19% of reference with a coverageData >= 49X There is a 4.91% of reference with a coverageData >= 50X There is a 4.64% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4296787386 17.23882319234021 370.89112890392653 chr2 243199373 4320634253 17.76581164541078 83.7292887915411 chr3 198022430 3570494120 18.0307560108216 23.385358609693032 chr4 191154276 3582104755 18.73933887306816 96.68848467484847 chr5 180915260 3299585879 18.238294984071548 20.65646598816296 chr6 171115067 3016764877 17.63003650052628 68.17693761051633 chr7 159138663 2834957285 17.814384207815042 99.1828210745838 chr8 146364022 2712223579 18.530671280678526 47.08725259753665 chr9 141213431 2153932135 15.253026002887784 111.87570184786505 chr10 135534747 2676945401 19.750989766484015 230.2017291797576 chr11 135006516 2428745606 17.989839882987575 87.43354451101403 chr12 133851895 2382744063 17.801347250257457 37.09266921610415 chr13 115169878 1718806807 14.924100266911806 17.68458298749532 chr14 107349540 1535580518 14.304490899541815 19.7425093673595 chr15 102531392 1388482552 13.542023812570495 23.244999610165348 chr16 90354753 1506656908 16.674904838708375 48.08421588039698 chr17 81195210 1433036138 17.64926943350476 89.10688226261195 chr18 78077248 1480811403 18.965978449957664 159.94785536130635 chr19 59128983 992588041 16.786827552910896 186.6138816642836 chr20 63025520 1102758530 17.497015970673466 30.79356674180345 chr21 48129895 703005172 14.606413996955531 59.13914861817049 chr22 51304566 628384871 12.248127603301429 48.03766905189812 chrMT 16571 53318794 3217.5966447408123 582.1572016847574 chrX 155270560 1460151753 9.403918894863263 35.20095994557479 chrY 59373566 525823988 8.856196846926796 180.88793119430915