BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264630.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 = 1,830,176,318 number of mapped reads = 1,817,650,518 (99.32%) number of supplementary alignments = 10,698,105 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 912,822,306 number of mapped paired reads (second in pair) = 904,828,212 number of mapped paired reads (both in pair) = 1,808,293,024 number of mapped paired reads (singletons) = 9,357,494 number of mapped bases = 182,549,955,596 bp number of sequenced bases = 182,507,883,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 799,548,869 duplication rate = 43.31% >>>>>>> Insert size mean insert size = 70,910.6556 std insert size = 2,566,463.0503 median insert size = 304 >>>>>>> Mapping quality mean mapping quality = 54.487 >>>>>>> ACTG content number of A's = 56,587,480,003 bp (31.01%) number of C's = 34,560,398,776 bp (18.94%) number of T's = 56,472,256,241 bp (30.94%) number of G's = 34,851,417,510 bp (19.1%) number of N's = 36,330,881 bp (0.02%) GC percentage = 38.03% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 765,640,701 number of insertions = 20,182,302 mapped reads with insertion percentage = 1.1% number of deletions = 18,894,857 mapped reads with deletion percentage = 1.02% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 58.969X std coverageData = 63.8368X There is a 90.4% of reference with a coverageData >= 1X There is a 89.01% of reference with a coverageData >= 2X There is a 87.72% of reference with a coverageData >= 3X There is a 86.48% of reference with a coverageData >= 4X There is a 85.28% of reference with a coverageData >= 5X There is a 84.1% of reference with a coverageData >= 6X There is a 82.94% of reference with a coverageData >= 7X There is a 81.79% of reference with a coverageData >= 8X There is a 80.67% of reference with a coverageData >= 9X There is a 79.55% of reference with a coverageData >= 10X There is a 78.45% of reference with a coverageData >= 11X There is a 77.37% of reference with a coverageData >= 12X There is a 76.3% of reference with a coverageData >= 13X There is a 75.24% of reference with a coverageData >= 14X There is a 74.19% of reference with a coverageData >= 15X There is a 73.15% of reference with a coverageData >= 16X There is a 72.13% of reference with a coverageData >= 17X There is a 71.11% of reference with a coverageData >= 18X There is a 70.11% of reference with a coverageData >= 19X There is a 69.12% of reference with a coverageData >= 20X There is a 68.14% of reference with a coverageData >= 21X There is a 67.17% of reference with a coverageData >= 22X There is a 66.21% of reference with a coverageData >= 23X There is a 65.25% of reference with a coverageData >= 24X There is a 64.31% of reference with a coverageData >= 25X There is a 63.38% of reference with a coverageData >= 26X There is a 62.46% of reference with a coverageData >= 27X There is a 61.55% of reference with a coverageData >= 28X There is a 60.65% of reference with a coverageData >= 29X There is a 59.75% of reference with a coverageData >= 30X There is a 58.87% of reference with a coverageData >= 31X There is a 58% of reference with a coverageData >= 32X There is a 57.13% of reference with a coverageData >= 33X There is a 56.27% of reference with a coverageData >= 34X There is a 55.43% of reference with a coverageData >= 35X There is a 54.59% of reference with a coverageData >= 36X There is a 53.76% of reference with a coverageData >= 37X There is a 52.94% of reference with a coverageData >= 38X There is a 52.14% of reference with a coverageData >= 39X There is a 51.34% of reference with a coverageData >= 40X There is a 50.55% of reference with a coverageData >= 41X There is a 49.76% of reference with a coverageData >= 42X There is a 48.99% of reference with a coverageData >= 43X There is a 48.23% of reference with a coverageData >= 44X There is a 47.48% of reference with a coverageData >= 45X There is a 46.73% of reference with a coverageData >= 46X There is a 46% of reference with a coverageData >= 47X There is a 45.27% of reference with a coverageData >= 48X There is a 44.56% of reference with a coverageData >= 49X There is a 43.85% of reference with a coverageData >= 50X There is a 43.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14272066750 57.259904479836784 65.32692554848329 chr2 243199373 16904465309 69.5086714265501 66.58253054916796 chr3 198022430 13895602412 70.17186089474814 63.41392514133504 chr4 191154276 15440790704 80.77659065288186 68.33820398409676 chr5 180915260 13168320328 72.78722827471823 64.73422704979875 chr6 171115067 13384517661 78.219398768666 72.01246873231035 chr7 159138663 11026588404 69.28918589695579 70.07377024066487 chr8 146364022 9458699454 64.62448438319083 61.42070884990332 chr9 141213431 7939994125 56.226904684441806 66.90867091647117 chr10 135534747 7862569157 58.0114644475634 59.72226890803572 chr11 135006516 8164082020 60.47176285920896 61.67270636741348 chr12 133851895 8447025941 63.10725702463906 66.29112486346496 chr13 115169878 6693689299 58.12013883526038 62.52264842856327 chr14 107349540 5657843783 52.704872168059595 62.217989607195115 chr15 102531392 4437634083 43.28073574774056 55.49797367389035 chr16 90354753 3326940793 36.820871980027434 48.09032270919613 chr17 81195210 2854228132 35.152666419607755 47.62608590641881 chr18 78077248 5143234480 65.87366501442264 62.63462646546179 chr19 59128983 1281537192 21.67358758732583 33.47950674048343 chr20 63025520 2769093625 43.936069468367734 60.56783144288295 chr21 48129895 2296742682 47.71966949024094 67.25963840387791 chr22 51304566 942397128 18.368679466073253 34.64144218154473 chrMT 16571 89934 5.4271920825538595 7.787229129707182 chrX 155270560 6371937616 41.03764175256404 45.28179936841037 chrY 59373566 809864584 13.640154003887858 32.48314910234576