BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672010.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 471,619,134 number of mapped reads = 431,627,279 (91.52%) number of supplementary alignments = 2,045,399 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 215,877,097 number of mapped paired reads (second in pair) = 215,750,182 number of mapped paired reads (both in pair) = 430,689,798 number of mapped paired reads (singletons) = 937,481 number of mapped bases = 63,959,242,767 bp number of sequenced bases = 63,932,139,149 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,193,964 duplication rate = 17.07% >>>>>>> Insert size mean insert size = 32,967.7387 std insert size = 1,692,289.1868 median insert size = 371 >>>>>>> Mapping quality mean mapping quality = 54.6013 >>>>>>> ACTG content number of A's = 19,024,286,344 bp (29.76%) number of C's = 12,984,647,665 bp (20.31%) number of T's = 18,863,770,359 bp (29.51%) number of G's = 13,059,139,329 bp (20.43%) number of N's = 295,452 bp (0%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 415,424,601 number of insertions = 9,239,724 mapped reads with insertion percentage = 2.02% number of deletions = 9,710,589 mapped reads with deletion percentage = 2.15% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 20.6607X std coverageData = 208.8137X There is a 92.33% of reference with a coverageData >= 1X There is a 92.28% of reference with a coverageData >= 2X There is a 92.21% of reference with a coverageData >= 3X There is a 92.11% of reference with a coverageData >= 4X There is a 91.94% of reference with a coverageData >= 5X There is a 91.67% of reference with a coverageData >= 6X There is a 91.26% of reference with a coverageData >= 7X There is a 90.71% of reference with a coverageData >= 8X There is a 89.97% of reference with a coverageData >= 9X There is a 89.04% of reference with a coverageData >= 10X There is a 87.86% of reference with a coverageData >= 11X There is a 86.41% of reference with a coverageData >= 12X There is a 84.58% of reference with a coverageData >= 13X There is a 82.31% of reference with a coverageData >= 14X There is a 79.48% of reference with a coverageData >= 15X There is a 76.04% of reference with a coverageData >= 16X There is a 71.93% of reference with a coverageData >= 17X There is a 67.18% of reference with a coverageData >= 18X There is a 61.85% of reference with a coverageData >= 19X There is a 56.07% of reference with a coverageData >= 20X There is a 50.01% of reference with a coverageData >= 21X There is a 43.85% of reference with a coverageData >= 22X There is a 37.79% of reference with a coverageData >= 23X There is a 32% of reference with a coverageData >= 24X There is a 26.63% of reference with a coverageData >= 25X There is a 21.79% of reference with a coverageData >= 26X There is a 17.54% of reference with a coverageData >= 27X There is a 13.91% of reference with a coverageData >= 28X There is a 10.87% of reference with a coverageData >= 29X There is a 8.39% of reference with a coverageData >= 30X There is a 6.41% of reference with a coverageData >= 31X There is a 4.86% of reference with a coverageData >= 32X There is a 3.68% of reference with a coverageData >= 33X There is a 2.78% of reference with a coverageData >= 34X There is a 2.12% of reference with a coverageData >= 35X There is a 1.63% of reference with a coverageData >= 36X There is a 1.28% of reference with a coverageData >= 37X There is a 1.03% of reference with a coverageData >= 38X There is a 0.85% of reference with a coverageData >= 39X There is a 0.72% of reference with a coverageData >= 40X There is a 0.63% of reference with a coverageData >= 41X There is a 0.56% of reference with a coverageData >= 42X There is a 0.51% of reference with a coverageData >= 43X There is a 0.48% of reference with a coverageData >= 44X There is a 0.45% of reference with a coverageData >= 45X There is a 0.42% of reference with a coverageData >= 46X There is a 0.4% of reference with a coverageData >= 47X There is a 0.39% of reference with a coverageData >= 48X There is a 0.37% of reference with a coverageData >= 49X There is a 0.36% of reference with a coverageData >= 50X There is a 0.35% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5236849867 21.0103784134604 455.4867810537432 chr2 243199373 5547596528 22.81089979619314 117.98992704806749 chr3 198022430 4294017540 21.68450079114775 13.936829042228954 chr4 191154276 4368486542 22.853198125685662 171.19909542806755 chr5 180915260 3919109383 21.662679991726513 15.59804297771638 chr6 171115067 3732590413 21.813335777146964 68.62500317965956 chr7 159138663 3503388546 22.014691338710065 166.91865066845372 chr8 146364022 3269755861 22.33988801564909 272.8570638542212 chr9 141213431 2776132711 19.65912655291266 277.3147673507174 chr10 135534747 3378556556 24.92760440243416 473.24231461891856 chr11 135006516 2962230631 21.941390080757287 115.3968738785773 chr12 133851895 2852048707 21.30749592301252 16.086090431045555 chr13 115169878 2102068687 18.25189644639547 11.854628720149613 chr14 107349540 1938392308 18.056829195541965 14.323693150891428 chr15 102531392 1824053952 17.79019982484974 12.182469915811716 chr16 90354753 1964891209 21.74640673302488 139.5999848971383 chr17 81195210 1755686676 21.623032639486986 99.96449366603592 chr18 78077248 1819452712 23.30323824938092 272.16739726731583 chr19 59128983 1257265708 21.26310388257481 209.44084586342126 chr20 63025520 1334115791 21.16786646107799 62.96524468482917 chr21 48129895 918135910 19.076208456303508 95.9665274232811 chr22 51304566 783692973 15.275306548738762 78.23974881579252 chrMT 16571 30841679 1861.183935791443 181.6062862154086 chrX 155270560 1719835427 11.076378078368494 32.503990453921766 chrY 59373566 670046450 11.28526539908349 215.42525472923603