BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976562.sorted.bam outfile = /home/yangyx/scDNA/SRP067062/SRP067062.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 = 366,809,340 number of mapped reads = 364,368,464 (99.33%) number of supplementary alignments = 11,877,237 (3.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,989,933 number of mapped paired reads (second in pair) = 181,378,531 number of mapped paired reads (both in pair) = 362,401,446 number of mapped paired reads (singletons) = 1,967,018 number of mapped bases = 84,410,489,785 bp number of sequenced bases = 84,381,620,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,082,421 duplication rate = 12.13% >>>>>>> Insert size mean insert size = 77,911.8321 std insert size = 2,714,739.6335 median insert size = 541 >>>>>>> Mapping quality mean mapping quality = 55.5314 >>>>>>> ACTG content number of A's = 24,428,400,488 bp (28.95%) number of C's = 17,729,760,602 bp (21.01%) number of T's = 24,261,536,176 bp (28.75%) number of G's = 17,960,420,184 bp (21.28%) number of N's = 1,503,134 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 572,250,701 number of insertions = 8,127,606 mapped reads with insertion percentage = 2.12% number of deletions = 10,546,029 mapped reads with deletion percentage = 2.76% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 27.2671X std coverageData = 41.8476X There is a 92.01% of reference with a coverageData >= 1X There is a 91.53% of reference with a coverageData >= 2X There is a 90.88% of reference with a coverageData >= 3X There is a 90.04% of reference with a coverageData >= 4X There is a 88.98% of reference with a coverageData >= 5X There is a 87.7% of reference with a coverageData >= 6X There is a 86.21% of reference with a coverageData >= 7X There is a 84.52% of reference with a coverageData >= 8X There is a 82.65% of reference with a coverageData >= 9X There is a 80.62% of reference with a coverageData >= 10X There is a 78.44% of reference with a coverageData >= 11X There is a 76.16% of reference with a coverageData >= 12X There is a 73.78% of reference with a coverageData >= 13X There is a 71.33% of reference with a coverageData >= 14X There is a 68.84% of reference with a coverageData >= 15X There is a 66.31% of reference with a coverageData >= 16X There is a 63.78% of reference with a coverageData >= 17X There is a 61.25% of reference with a coverageData >= 18X There is a 58.75% of reference with a coverageData >= 19X There is a 56.28% of reference with a coverageData >= 20X There is a 53.86% of reference with a coverageData >= 21X There is a 51.49% of reference with a coverageData >= 22X There is a 49.18% of reference with a coverageData >= 23X There is a 46.94% of reference with a coverageData >= 24X There is a 44.77% of reference with a coverageData >= 25X There is a 42.68% of reference with a coverageData >= 26X There is a 40.66% of reference with a coverageData >= 27X There is a 38.72% of reference with a coverageData >= 28X There is a 36.85% of reference with a coverageData >= 29X There is a 35.06% of reference with a coverageData >= 30X There is a 33.35% of reference with a coverageData >= 31X There is a 31.71% of reference with a coverageData >= 32X There is a 30.15% of reference with a coverageData >= 33X There is a 28.66% of reference with a coverageData >= 34X There is a 27.23% of reference with a coverageData >= 35X There is a 25.88% of reference with a coverageData >= 36X There is a 24.59% of reference with a coverageData >= 37X There is a 23.37% of reference with a coverageData >= 38X There is a 22.2% of reference with a coverageData >= 39X There is a 21.09% of reference with a coverageData >= 40X There is a 20.04% of reference with a coverageData >= 41X There is a 19.04% of reference with a coverageData >= 42X There is a 18.1% of reference with a coverageData >= 43X There is a 17.2% of reference with a coverageData >= 44X There is a 16.35% of reference with a coverageData >= 45X There is a 15.55% of reference with a coverageData >= 46X There is a 14.78% of reference with a coverageData >= 47X There is a 14.06% of reference with a coverageData >= 48X There is a 13.37% of reference with a coverageData >= 49X There is a 12.73% of reference with a coverageData >= 50X There is a 12.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7262396556 29.136924621744473 67.27815707354459 chr2 243199373 7001819580 28.79045078788094 31.75698240008184 chr3 198022430 5788309094 29.23057299115055 21.605054817793526 chr4 191154276 4084877148 21.369530587952948 18.208857642220963 chr5 180915260 5339825418 29.51561641621608 22.82454930054889 chr6 171115067 5247989373 30.669358724559306 35.77840279605608 chr7 159138663 4807514383 30.209593899880886 27.0811110869395 chr8 146364022 4143567007 28.310010550270338 23.6106174042571 chr9 141213431 3785208621 26.80487680382187 85.9498449352618 chr10 135534747 4013880696 29.615141392487345 62.06068813261334 chr11 135006516 3891896876 28.82747434205324 31.688930848146747 chr12 133851895 4052169636 30.273532070651672 25.466925381124287 chr13 115169878 2167081642 18.816392616131797 18.069003814711145 chr14 107349540 2835142414 26.410382513050358 24.922665794550667 chr15 102531392 2546366004 24.83498911240764 24.037766487197757 chr16 90354753 2811910267 31.120778637953887 28.935465686329 chr17 81195210 3146004563 38.74618420224543 70.8429938187522 chr18 78077248 2138165929 27.385262464681134 77.04644294227818 chr19 59128983 2196478631 37.1472418357001 51.33367220974593 chr20 63025520 2289745942 36.330456964099625 30.24379848790366 chr21 48129895 1061835381 22.061867805861617 28.542100415265264 chr22 51304566 1413169503 27.5447121607071 30.964800349410954 chrMT 16571 990037 59.74515720234144 21.468043019183803 chrX 155270560 2024842462 13.040736518242737 14.701540324444334 chrY 59373566 359302622 6.051558735751192 26.05359655722976