BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264628.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 = 1,225,488,472 number of mapped reads = 1,217,642,116 (99.36%) number of supplementary alignments = 6,803,858 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 610,212,176 number of mapped paired reads (second in pair) = 607,429,940 number of mapped paired reads (both in pair) = 1,213,771,056 number of mapped paired reads (singletons) = 3,871,060 number of mapped bases = 122,298,213,217 bp number of sequenced bases = 122,270,105,316 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 427,868,429 duplication rate = 34.86% >>>>>>> Insert size mean insert size = 69,215.9139 std insert size = 2,523,721.9612 median insert size = 310 >>>>>>> Mapping quality mean mapping quality = 54.5855 >>>>>>> ACTG content number of A's = 37,847,978,075 bp (30.95%) number of C's = 23,254,309,179 bp (19.02%) number of T's = 37,731,069,597 bp (30.86%) number of G's = 23,421,429,933 bp (19.16%) number of N's = 15,318,532 bp (0.01%) GC percentage = 38.17% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 425,840,868 number of insertions = 13,540,100 mapped reads with insertion percentage = 1.1% number of deletions = 12,633,394 mapped reads with deletion percentage = 1.02% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 39.5059X std coverageData = 39.962X There is a 90.37% of reference with a coverageData >= 1X There is a 88.81% of reference with a coverageData >= 2X There is a 87.28% of reference with a coverageData >= 3X There is a 85.76% of reference with a coverageData >= 4X There is a 84.25% of reference with a coverageData >= 5X There is a 82.74% of reference with a coverageData >= 6X There is a 81.23% of reference with a coverageData >= 7X There is a 79.74% of reference with a coverageData >= 8X There is a 78.25% of reference with a coverageData >= 9X There is a 76.78% of reference with a coverageData >= 10X There is a 75.31% of reference with a coverageData >= 11X There is a 73.86% of reference with a coverageData >= 12X There is a 72.41% of reference with a coverageData >= 13X There is a 70.98% of reference with a coverageData >= 14X There is a 69.56% of reference with a coverageData >= 15X There is a 68.15% of reference with a coverageData >= 16X There is a 66.76% of reference with a coverageData >= 17X There is a 65.38% of reference with a coverageData >= 18X There is a 64.01% of reference with a coverageData >= 19X There is a 62.66% of reference with a coverageData >= 20X There is a 61.32% of reference with a coverageData >= 21X There is a 59.99% of reference with a coverageData >= 22X There is a 58.69% of reference with a coverageData >= 23X There is a 57.4% of reference with a coverageData >= 24X There is a 56.12% of reference with a coverageData >= 25X There is a 54.86% of reference with a coverageData >= 26X There is a 53.62% of reference with a coverageData >= 27X There is a 52.4% of reference with a coverageData >= 28X There is a 51.19% of reference with a coverageData >= 29X There is a 50% of reference with a coverageData >= 30X There is a 48.83% of reference with a coverageData >= 31X There is a 47.68% of reference with a coverageData >= 32X There is a 46.55% of reference with a coverageData >= 33X There is a 45.43% of reference with a coverageData >= 34X There is a 44.34% of reference with a coverageData >= 35X There is a 43.26% of reference with a coverageData >= 36X There is a 42.2% of reference with a coverageData >= 37X There is a 41.16% of reference with a coverageData >= 38X There is a 40.14% of reference with a coverageData >= 39X There is a 39.14% of reference with a coverageData >= 40X There is a 38.16% of reference with a coverageData >= 41X There is a 37.19% of reference with a coverageData >= 42X There is a 36.25% of reference with a coverageData >= 43X There is a 35.32% of reference with a coverageData >= 44X There is a 34.42% of reference with a coverageData >= 45X There is a 33.53% of reference with a coverageData >= 46X There is a 32.66% of reference with a coverageData >= 47X There is a 31.82% of reference with a coverageData >= 48X There is a 30.98% of reference with a coverageData >= 49X There is a 30.17% of reference with a coverageData >= 50X There is a 29.38% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9763091833 39.16977937238519 41.514697297467976 chr2 243199373 10505096381 43.1954089824072 40.49840080527203 chr3 198022430 9663571216 48.80038698646411 39.76850886760845 chr4 191154276 10071978795 52.690313843672534 40.988636538216234 chr5 180915260 8424967701 46.5685852094511 38.57746215645358 chr6 171115067 8654274418 50.575759164445756 43.11223716178179 chr7 159138663 7047160449 44.283144750311244 41.30180243831862 chr8 146364022 7021711934 47.974302960873814 40.48493386651613 chr9 141213431 5321375787 37.68321291619917 43.5539262317928 chr10 135534747 5219234905 38.50846384801972 36.710803993100726 chr11 135006516 5575337539 41.29680332614464 41.31384853301742 chr12 133851895 5800606518 43.33600594896322 41.965685617426814 chr13 115169878 4785592909 41.552470073815655 39.79180634927671 chr14 107349540 4065458294 37.87122230798567 40.6050319128834 chr15 102531392 3178432298 30.999601546421996 36.23060558960503 chr16 90354753 2209929180 24.458361144543222 30.69276074063964 chr17 81195210 1994405816 24.56309696101531 30.67157082079357 chr18 78077248 3539354124 45.33144052413323 38.853423998633495 chr19 59128983 851750035 14.404949853441586 21.73164578429972 chr20 63025520 1869488883 29.66241108363723 40.170631624972046 chr21 48129895 1542667361 32.05216551999542 42.004510457860505 chr22 51304566 680837605 13.27050705389458 22.512567659973286 chrMT 16571 73506 4.435821616076278 7.788608117509478 chrX 155270560 3892936217 25.07195322152506 26.24662388019052 chrY 59373566 618879513 10.4234856467944 22.75230155516152