BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671989.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 = 284,188,530 number of mapped reads = 280,959,254 (98.86%) number of supplementary alignments = 1,301,856 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 140,431,641 number of mapped paired reads (second in pair) = 140,527,613 number of mapped paired reads (both in pair) = 280,456,556 number of mapped paired reads (singletons) = 502,698 number of mapped bases = 39,986,034,498 bp number of sequenced bases = 39,970,129,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,259,383 duplication rate = 30.29% >>>>>>> Insert size mean insert size = 32,934.6839 std insert size = 1,710,507.7248 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 54.3692 >>>>>>> ACTG content number of A's = 12,106,055,679 bp (30.29%) number of C's = 7,887,428,258 bp (19.73%) number of T's = 12,042,758,204 bp (30.13%) number of G's = 7,933,586,164 bp (19.85%) number of N's = 301,509 bp (0%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 217,171,942 number of insertions = 5,299,578 mapped reads with insertion percentage = 1.8% number of deletions = 5,889,367 mapped reads with deletion percentage = 1.99% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 12.9167X std coverageData = 178.1902X There is a 91.49% of reference with a coverageData >= 1X There is a 91.03% of reference with a coverageData >= 2X There is a 90.12% of reference with a coverageData >= 3X There is a 88.69% of reference with a coverageData >= 4X There is a 86.59% of reference with a coverageData >= 5X There is a 83.77% of reference with a coverageData >= 6X There is a 80.2% of reference with a coverageData >= 7X There is a 75.92% of reference with a coverageData >= 8X There is a 70.99% of reference with a coverageData >= 9X There is a 65.53% of reference with a coverageData >= 10X There is a 59.71% of reference with a coverageData >= 11X There is a 53.67% of reference with a coverageData >= 12X There is a 47.6% of reference with a coverageData >= 13X There is a 41.64% of reference with a coverageData >= 14X There is a 35.95% of reference with a coverageData >= 15X There is a 30.64% of reference with a coverageData >= 16X There is a 25.77% of reference with a coverageData >= 17X There is a 21.42% of reference with a coverageData >= 18X There is a 17.59% of reference with a coverageData >= 19X There is a 14.28% of reference with a coverageData >= 20X There is a 11.47% of reference with a coverageData >= 21X There is a 9.12% of reference with a coverageData >= 22X There is a 7.19% of reference with a coverageData >= 23X There is a 5.63% of reference with a coverageData >= 24X There is a 4.38% of reference with a coverageData >= 25X There is a 3.39% of reference with a coverageData >= 26X There is a 2.61% of reference with a coverageData >= 27X There is a 2.01% of reference with a coverageData >= 28X There is a 1.55% of reference with a coverageData >= 29X There is a 1.21% of reference with a coverageData >= 30X There is a 0.95% of reference with a coverageData >= 31X There is a 0.75% of reference with a coverageData >= 32X There is a 0.6% of reference with a coverageData >= 33X There is a 0.49% of reference with a coverageData >= 34X There is a 0.41% of reference with a coverageData >= 35X There is a 0.36% of reference with a coverageData >= 36X There is a 0.31% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3087818009 12.388406482646236 406.6312387081085 chr2 243199373 3559713601 14.637018003331777 107.6644543071112 chr3 198022430 2801049579 14.145112647087505 11.467552747687806 chr4 191154276 2957781011 15.47326626896905 67.85863567642356 chr5 180915260 2568233288 14.195780322787586 11.780249244307317 chr6 171115067 2472604316 14.449950897661163 90.56663642129772 chr7 159138663 2184437291 13.72662839953607 89.64659576477011 chr8 146364022 2148705455 14.680557596319675 395.2681638115688 chr9 141213431 1672532863 11.8440069840099 212.73225438808888 chr10 135534747 2017015598 14.881907722157772 300.6747595868015 chr11 135006516 1756934281 13.013699879493224 67.81822431284003 chr12 133851895 1771811513 13.237104435465781 80.86160900868471 chr13 115169878 1420444619 12.333473332323926 8.327959464223936 chr14 107349540 1184104175 11.030360959162005 13.423515504071338 chr15 102531392 1017317837 9.92201331861368 14.88072431563858 chr16 90354753 1064839714 11.785099052841193 116.38749761881402 chr17 81195210 852968957 10.50516350656646 76.88724432536902 chr18 78077248 1164078132 14.909313043410547 198.285769925852 chr19 59128983 533862749 9.028782872859491 184.16865384648335 chr20 63025520 689146311 10.93440103310532 26.41278454590179 chr21 48129895 541291243 11.246466317867512 35.21275771555588 chr22 51304566 315311437 6.145874755085152 12.977422652739888 chrMT 16571 52032692 3139.9850340957096 351.3008811180529 chrX 155270560 2057572264 13.25152858339662 32.06098273118655 chrY 59373566 94427563 1.590397366397026 77.56623380422118