BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671998.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 = 493,634,322 number of mapped reads = 327,436,445 (66.33%) number of supplementary alignments = 5,794,044 (1.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 163,744,447 number of mapped paired reads (second in pair) = 163,691,998 number of mapped paired reads (both in pair) = 326,082,662 number of mapped paired reads (singletons) = 1,353,783 number of mapped bases = 44,805,232,159 bp number of sequenced bases = 44,786,304,478 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,462,966 duplication rate = 40.77% >>>>>>> Insert size mean insert size = 66,351.8291 std insert size = 2,471,911.7233 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 54.0383 >>>>>>> ACTG content number of A's = 13,423,869,560 bp (29.97%) number of C's = 9,061,646,818 bp (20.23%) number of T's = 13,249,236,368 bp (29.58%) number of G's = 9,051,111,793 bp (20.21%) number of N's = 439,939 bp (0%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 249,742,422 number of insertions = 6,497,493 mapped reads with insertion percentage = 1.86% number of deletions = 6,678,788 mapped reads with deletion percentage = 1.94% homopolymer indels = 43.75% >>>>>>> Coverage mean coverageData = 14.4734X std coverageData = 200.4982X There is a 91.57% of reference with a coverageData >= 1X There is a 91.36% of reference with a coverageData >= 2X There is a 90.89% of reference with a coverageData >= 3X There is a 90.15% of reference with a coverageData >= 4X There is a 88.92% of reference with a coverageData >= 5X There is a 87.14% of reference with a coverageData >= 6X There is a 84.66% of reference with a coverageData >= 7X There is a 81.48% of reference with a coverageData >= 8X There is a 77.55% of reference with a coverageData >= 9X There is a 72.97% of reference with a coverageData >= 10X There is a 67.81% of reference with a coverageData >= 11X There is a 62.23% of reference with a coverageData >= 12X There is a 56.38% of reference with a coverageData >= 13X There is a 50.44% of reference with a coverageData >= 14X There is a 44.54% of reference with a coverageData >= 15X There is a 38.86% of reference with a coverageData >= 16X There is a 33.49% of reference with a coverageData >= 17X There is a 28.53% of reference with a coverageData >= 18X There is a 24.04% of reference with a coverageData >= 19X There is a 20.04% of reference with a coverageData >= 20X There is a 16.54% of reference with a coverageData >= 21X There is a 13.53% of reference with a coverageData >= 22X There is a 10.97% of reference with a coverageData >= 23X There is a 8.82% of reference with a coverageData >= 24X There is a 7.05% of reference with a coverageData >= 25X There is a 5.6% of reference with a coverageData >= 26X There is a 4.43% of reference with a coverageData >= 27X There is a 3.5% of reference with a coverageData >= 28X There is a 2.75% of reference with a coverageData >= 29X There is a 2.17% of reference with a coverageData >= 30X There is a 1.72% of reference with a coverageData >= 31X There is a 1.37% of reference with a coverageData >= 32X There is a 1.1% of reference with a coverageData >= 33X There is a 0.89% of reference with a coverageData >= 34X There is a 0.73% of reference with a coverageData >= 35X There is a 0.61% of reference with a coverageData >= 36X There is a 0.52% of reference with a coverageData >= 37X There is a 0.45% of reference with a coverageData >= 38X There is a 0.39% of reference with a coverageData >= 39X There is a 0.35% of reference with a coverageData >= 40X There is a 0.32% of reference with a coverageData >= 41X There is a 0.29% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.25% of reference with a coverageData >= 44X There is a 0.24% of reference with a coverageData >= 45X There is a 0.23% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3650374795 14.645398997822356 519.9811405543059 chr2 243199373 3826906933 15.73567762857678 109.8079882722118 chr3 198022430 2954099358 14.918003773612918 19.088750190111025 chr4 191154276 3058570050 16.00053168572593 154.36735304691103 chr5 180915260 2686117817 14.847381127495824 12.949799614981961 chr6 171115067 2585314255 15.108630118468762 67.58588289599557 chr7 159138663 2419178706 15.201703095871807 159.92399438331302 chr8 146364022 2234295057 15.265329733833086 160.7324368699912 chr9 141213431 1906945794 13.503997321614543 209.12196015913466 chr10 135534747 2365338242 17.451895505438173 395.77684555886555 chr11 135006516 2008163752 14.874569105983003 71.72927689028343 chr12 133851895 1961454585 14.653917189592272 33.15850430633312 chr13 115169878 1434334379 12.454075700245163 8.686436187126398 chr14 107349540 1324713946 12.340192105154806 12.968412823915275 chr15 102531392 1229130724 11.987847819329323 11.494775707087177 chr16 90354753 1372797931 15.193422431247198 133.59311954124408 chr17 81195210 1192242640 14.683657324120475 94.5549090974493 chr18 78077248 1251874716 16.03379663176653 212.22224462901804 chr19 59128983 852025395 14.409606791309095 259.4789022806152 chr20 63025520 894299440 14.189481340257089 58.65626896457906 chr21 48129895 620869400 12.899870236575417 88.57138733242166 chr22 51304566 495248096 9.653099804021341 12.361082797483022 chrMT 16571 57335308 3459.9787580713296 420.5768267114588 chrX 155270560 2272988369 14.638888202631588 38.924882929425664 chrY 59373566 150612471 2.5366923556520087 166.95330694822897