BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781853.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 368,621,820 number of mapped reads = 354,135,047 (96.07%) number of supplementary alignments = 920,077 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 178,498,201 number of mapped paired reads (second in pair) = 175,636,846 number of mapped paired reads (both in pair) = 348,471,806 number of mapped paired reads (singletons) = 5,663,241 number of mapped bases = 35,148,693,293 bp number of sequenced bases = 35,141,838,864 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,766,198 duplication rate = 11.61% >>>>>>> Insert size mean insert size = 28,630.5469 std insert size = 1,636,375.3475 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 53.9376 >>>>>>> ACTG content number of A's = 10,392,736,643 bp (29.57%) number of C's = 7,179,400,924 bp (20.43%) number of T's = 10,310,688,581 bp (29.34%) number of G's = 7,249,948,795 bp (20.63%) number of N's = 9,063,921 bp (0.03%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 169,885,856 number of insertions = 3,546,541 mapped reads with insertion percentage = 0.99% number of deletions = 3,010,382 mapped reads with deletion percentage = 0.83% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 11.3541X std coverageData = 13.4652X There is a 88.98% of reference with a coverageData >= 1X There is a 85.22% of reference with a coverageData >= 2X There is a 80.53% of reference with a coverageData >= 3X There is a 75.29% of reference with a coverageData >= 4X There is a 69.77% of reference with a coverageData >= 5X There is a 64.2% of reference with a coverageData >= 6X There is a 58.76% of reference with a coverageData >= 7X There is a 53.56% of reference with a coverageData >= 8X There is a 48.68% of reference with a coverageData >= 9X There is a 44.16% of reference with a coverageData >= 10X There is a 40% of reference with a coverageData >= 11X There is a 36.21% of reference with a coverageData >= 12X There is a 32.76% of reference with a coverageData >= 13X There is a 29.65% of reference with a coverageData >= 14X There is a 26.84% of reference with a coverageData >= 15X There is a 24.31% of reference with a coverageData >= 16X There is a 22.03% of reference with a coverageData >= 17X There is a 19.99% of reference with a coverageData >= 18X There is a 18.15% of reference with a coverageData >= 19X There is a 16.5% of reference with a coverageData >= 20X There is a 15.01% of reference with a coverageData >= 21X There is a 13.68% of reference with a coverageData >= 22X There is a 12.48% of reference with a coverageData >= 23X There is a 11.39% of reference with a coverageData >= 24X There is a 10.41% of reference with a coverageData >= 25X There is a 9.53% of reference with a coverageData >= 26X There is a 8.73% of reference with a coverageData >= 27X There is a 8.01% of reference with a coverageData >= 28X There is a 7.35% of reference with a coverageData >= 29X There is a 6.76% of reference with a coverageData >= 30X There is a 6.22% of reference with a coverageData >= 31X There is a 5.73% of reference with a coverageData >= 32X There is a 5.29% of reference with a coverageData >= 33X There is a 4.88% of reference with a coverageData >= 34X There is a 4.51% of reference with a coverageData >= 35X There is a 4.17% of reference with a coverageData >= 36X There is a 3.86% of reference with a coverageData >= 37X There is a 3.58% of reference with a coverageData >= 38X There is a 3.32% of reference with a coverageData >= 39X There is a 3.08% of reference with a coverageData >= 40X There is a 2.86% of reference with a coverageData >= 41X There is a 2.66% of reference with a coverageData >= 42X There is a 2.48% of reference with a coverageData >= 43X There is a 2.31% of reference with a coverageData >= 44X There is a 2.15% of reference with a coverageData >= 45X There is a 2.01% of reference with a coverageData >= 46X There is a 1.88% of reference with a coverageData >= 47X There is a 1.75% of reference with a coverageData >= 48X There is a 1.64% of reference with a coverageData >= 49X There is a 1.54% of reference with a coverageData >= 50X There is a 1.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2826138800 11.338542663049173 16.86346155680441 chr2 243199373 2947187601 12.1184013126547 14.958238510212711 chr3 198022430 1818590379 9.183759531685375 9.672581762655872 chr4 191154276 2308946169 12.078966881180309 11.91831811272404 chr5 180915260 2184725723 12.075961546859011 11.097309620216675 chr6 171115067 2117799011 12.376461337562986 12.367254730748234 chr7 159138663 1824732779 11.466307084658617 12.685930748070422 chr8 146364022 1786375196 12.20501576541809 11.742502984080692 chr9 141213431 1434105551 10.155588890124765 13.906731535352831 chr10 135534747 1960423105 14.464358021784628 17.91020766453379 chr11 135006516 1641668097 12.159917503537384 12.192611458822748 chr12 133851895 2384286881 17.81287355700119 16.58165779149318 chr13 115169878 1106000505 9.603209834085263 10.53436938684556 chr14 107349540 1052103315 9.800724949543334 11.288839985557127 chr15 102531392 973759802 9.497186988351821 11.320782361182937 chr16 90354753 821619525 9.09326291888596 11.10610430535641 chr17 81195210 735981570 9.064347145601323 10.75223428243286 chr18 78077248 911789505 11.678043583195965 13.194348844662946 chr19 59128983 481285031 8.139579045355811 12.08197652798978 chr20 63025520 674932290 10.70887300890179 13.411055530150605 chr21 48129895 428518282 8.903370389650757 15.577865896665656 chr22 51304566 308592112 6.01490541797001 9.241607120785778 chrMT 16571 699978 42.241144167521576 13.097739081449395 chrX 155270560 2385905552 15.366116744861356 14.82435423495603 chrY 59373566 32526534 0.5478285403979273 5.9322210345808175