BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781847.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 = 147,502,694 number of mapped reads = 139,951,731 (94.88%) number of supplementary alignments = 462,565 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 71,062,657 number of mapped paired reads (second in pair) = 68,889,074 number of mapped paired reads (both in pair) = 136,722,218 number of mapped paired reads (singletons) = 3,229,513 number of mapped bases = 13,850,521,355 bp number of sequenced bases = 13,847,292,866 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,906,933 duplication rate = 6.04% >>>>>>> Insert size mean insert size = 50,045.305 std insert size = 2,173,582.6749 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 53.8913 >>>>>>> ACTG content number of A's = 4,127,317,273 bp (29.81%) number of C's = 2,786,002,821 bp (20.12%) number of T's = 4,107,633,313 bp (29.66%) number of G's = 2,825,753,699 bp (20.41%) number of N's = 585,760 bp (0%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 55,896,814 number of insertions = 1,448,812 mapped reads with insertion percentage = 1.02% number of deletions = 1,450,570 mapped reads with deletion percentage = 1.02% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 4.4741X std coverageData = 7.1326X There is a 82.22% of reference with a coverageData >= 1X There is a 70.64% of reference with a coverageData >= 2X There is a 58.58% of reference with a coverageData >= 3X There is a 47.48% of reference with a coverageData >= 4X There is a 37.94% of reference with a coverageData >= 5X There is a 30.05% of reference with a coverageData >= 6X There is a 23.71% of reference with a coverageData >= 7X There is a 18.68% of reference with a coverageData >= 8X There is a 14.73% of reference with a coverageData >= 9X There is a 11.65% of reference with a coverageData >= 10X There is a 9.24% of reference with a coverageData >= 11X There is a 7.36% of reference with a coverageData >= 12X There is a 5.9% of reference with a coverageData >= 13X There is a 4.74% of reference with a coverageData >= 14X There is a 3.83% of reference with a coverageData >= 15X There is a 3.11% of reference with a coverageData >= 16X There is a 2.54% of reference with a coverageData >= 17X There is a 2.09% of reference with a coverageData >= 18X There is a 1.72% of reference with a coverageData >= 19X There is a 1.42% of reference with a coverageData >= 20X There is a 1.18% of reference with a coverageData >= 21X There is a 0.99% of reference with a coverageData >= 22X There is a 0.83% of reference with a coverageData >= 23X There is a 0.7% of reference with a coverageData >= 24X There is a 0.6% of reference with a coverageData >= 25X There is a 0.51% of reference with a coverageData >= 26X There is a 0.43% of reference with a coverageData >= 27X There is a 0.37% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 569559952 2.2850894000380446 6.263948219565531 chr2 243199373 1139597850 4.6858585034263225 16.346345533324637 chr3 198022430 987605028 4.987339201927782 4.553113287999506 chr4 191154276 927361622 4.851377857746693 4.88963685970725 chr5 180915260 836066208 4.621313912380857 4.377537064018422 chr6 171115067 834546762 4.8771085833137064 5.700448109512275 chr7 159138663 757725018 4.761413748964323 5.311727200290181 chr8 146364022 710767138 4.8561601976201505 4.591876061158094 chr9 141213431 610423031 4.322698107944137 5.895167920380028 chr10 135534747 789067966 5.821886884844371 9.629095354457336 chr11 135006516 648688099 4.804865114806755 4.888845230722905 chr12 133851895 967946603 7.23147478039067 7.112333557600431 chr13 115169878 420853890 3.654201057675862 4.191895891960251 chr14 107349540 432845314 4.032111492978918 4.568544728842908 chr15 102531392 398094755 3.88266215092447 4.556194890858829 chr16 90354753 345518266 3.8240187098956486 4.530582618441121 chr17 81195210 336517184 4.144544782875738 5.513709142250384 chr18 78077248 352721594 4.517597674549185 5.6449707229388535 chr19 59128983 215725154 3.6483826214294943 5.5682789251552425 chr20 63025520 276557372 4.388022058366198 5.183524029723038 chr21 48129895 177004450 3.6776404768803257 6.449703619557638 chr22 51304566 140319614 2.735031692890648 4.073904787207924 chrMT 16571 1462510 88.25719630680103 23.819867872281566 chrX 155270560 960226903 6.184217426664785 5.878301855261739 chrY 59373566 13319072 0.22432663047390483 2.382060769040187