BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264624.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,391,545,590 number of mapped reads = 1,384,958,187 (99.53%) number of supplementary alignments = 9,313,435 (0.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 694,283,598 number of mapped paired reads (second in pair) = 690,674,589 number of mapped paired reads (both in pair) = 1,380,302,262 number of mapped paired reads (singletons) = 4,655,925 number of mapped bases = 139,109,575,979 bp number of sequenced bases = 139,077,306,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 512,835,794 duplication rate = 36.42% >>>>>>> Insert size mean insert size = 91,318.5526 std insert size = 2,925,257.3362 median insert size = 315 >>>>>>> Mapping quality mean mapping quality = 54.4926 >>>>>>> ACTG content number of A's = 43,021,154,818 bp (30.93%) number of C's = 26,440,123,874 bp (19.01%) number of T's = 42,900,567,443 bp (30.85%) number of G's = 26,706,739,552 bp (19.2%) number of N's = 8,720,985 bp (0.01%) GC percentage = 38.21% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 509,937,520 number of insertions = 15,650,958 mapped reads with insertion percentage = 1.11% number of deletions = 14,547,266 mapped reads with deletion percentage = 1.03% homopolymer indels = 48.65% >>>>>>> Coverage mean coverageData = 44.9365X std coverageData = 47.9997X There is a 90.05% of reference with a coverageData >= 1X There is a 88.36% of reference with a coverageData >= 2X There is a 86.77% of reference with a coverageData >= 3X There is a 85.25% of reference with a coverageData >= 4X There is a 83.77% of reference with a coverageData >= 5X There is a 82.32% of reference with a coverageData >= 6X There is a 80.9% of reference with a coverageData >= 7X There is a 79.49% of reference with a coverageData >= 8X There is a 78.11% of reference with a coverageData >= 9X There is a 76.74% of reference with a coverageData >= 10X There is a 75.39% of reference with a coverageData >= 11X There is a 74.05% of reference with a coverageData >= 12X There is a 72.73% of reference with a coverageData >= 13X There is a 71.42% of reference with a coverageData >= 14X There is a 70.13% of reference with a coverageData >= 15X There is a 68.85% of reference with a coverageData >= 16X There is a 67.58% of reference with a coverageData >= 17X There is a 66.33% of reference with a coverageData >= 18X There is a 65.09% of reference with a coverageData >= 19X There is a 63.86% of reference with a coverageData >= 20X There is a 62.65% of reference with a coverageData >= 21X There is a 61.46% of reference with a coverageData >= 22X There is a 60.28% of reference with a coverageData >= 23X There is a 59.12% of reference with a coverageData >= 24X There is a 57.97% of reference with a coverageData >= 25X There is a 56.83% of reference with a coverageData >= 26X There is a 55.71% of reference with a coverageData >= 27X There is a 54.61% of reference with a coverageData >= 28X There is a 53.52% of reference with a coverageData >= 29X There is a 52.45% of reference with a coverageData >= 30X There is a 51.4% of reference with a coverageData >= 31X There is a 50.36% of reference with a coverageData >= 32X There is a 49.34% of reference with a coverageData >= 33X There is a 48.33% of reference with a coverageData >= 34X There is a 47.34% of reference with a coverageData >= 35X There is a 46.37% of reference with a coverageData >= 36X There is a 45.41% of reference with a coverageData >= 37X There is a 44.47% of reference with a coverageData >= 38X There is a 43.54% of reference with a coverageData >= 39X There is a 42.63% of reference with a coverageData >= 40X There is a 41.73% of reference with a coverageData >= 41X There is a 40.85% of reference with a coverageData >= 42X There is a 39.99% of reference with a coverageData >= 43X There is a 39.14% of reference with a coverageData >= 44X There is a 38.3% of reference with a coverageData >= 45X There is a 37.48% of reference with a coverageData >= 46X There is a 36.68% of reference with a coverageData >= 47X There is a 35.89% of reference with a coverageData >= 48X There is a 35.11% of reference with a coverageData >= 49X There is a 34.35% of reference with a coverageData >= 50X There is a 33.61% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11103102855 44.545938583639476 49.88005722007286 chr2 243199373 13251151868 54.48678466782067 50.795339881659544 chr3 198022430 11140417972 56.258364125720504 49.93036175936328 chr4 191154276 11763517880 61.53939177379427 51.35441128805774 chr5 180915260 9432452997 52.13740950873906 49.64903333300539 chr6 171115067 9583773724 56.00777238394793 51.37856726570649 chr7 159138663 7646290867 48.04797729763508 48.27609258498446 chr8 146364022 7821691875 53.43999002022505 48.36008211748186 chr9 141213431 5945373819 42.102042113826975 51.69003349280096 chr10 135534747 6299824963 46.481253718649725 45.01615624021293 chr11 135006516 6699712421 49.625104176453235 49.36701166089854 chr12 133851895 6366274118 47.56207686114567 48.20859385982623 chr13 115169878 4800693427 41.68358524266215 44.264751616240105 chr14 107349540 4122323223 38.40093979908996 44.144885382873255 chr15 102531392 3588228189 34.99638617019849 44.650695285995326 chr16 90354753 2841858303 31.45222811908965 38.36643771674941 chr17 81195210 2348305156 28.92172033300979 37.62298075849638 chr18 78077248 3662683242 46.911018713159564 43.1797198788449 chr19 59128983 950402374 16.07337596183584 23.793304010912486 chr20 63025520 2244776074 35.61693856710742 49.08504790453956 chr21 48129895 1663052898 34.55342875773986 47.0428245444806 chr22 51304566 746029081 14.541182962155844 25.909592310624216 chrMT 16571 70670 4.2646792589463525 8.771506536904226 chrX 155270560 4512500029 29.06217398198345 33.031353914020436 chrY 59373566 575067954 9.685588937002706 23.885655164049524