BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779098.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 27,356,658 number of mapped reads = 26,290,783 (96.1%) number of supplementary alignments = 145,692 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,257,929 number of mapped paired reads (second in pair) = 13,032,854 number of mapped paired reads (both in pair) = 25,948,456 number of mapped paired reads (singletons) = 342,327 number of mapped bases = 2,621,447,974 bp number of sequenced bases = 2,620,837,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,149,661 duplication rate = 3.72% >>>>>>> Insert size mean insert size = 62,294.8151 std insert size = 2,381,195.1971 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 53.4279 >>>>>>> ACTG content number of A's = 799,398,956 bp (30.5%) number of C's = 508,763,217 bp (19.41%) number of T's = 794,869,206 bp (30.33%) number of G's = 516,743,652 bp (19.72%) number of N's = 1,062,804 bp (0.04%) GC percentage = 39.13% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 11,120,009 number of insertions = 220,404 mapped reads with insertion percentage = 0.83% number of deletions = 272,637 mapped reads with deletion percentage = 1.02% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.8468X std coverageData = 2.9X There is a 31.86% of reference with a coverageData >= 1X There is a 18.15% of reference with a coverageData >= 2X There is a 10.73% of reference with a coverageData >= 3X There is a 6.78% of reference with a coverageData >= 4X There is a 4.43% of reference with a coverageData >= 5X There is a 2.99% of reference with a coverageData >= 6X There is a 2.07% of reference with a coverageData >= 7X There is a 1.46% of reference with a coverageData >= 8X There is a 1.05% of reference with a coverageData >= 9X There is a 0.77% of reference with a coverageData >= 10X There is a 0.57% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 159553620 0.6401332897782429 4.812625077898563 chr2 243199373 155232319 0.6382924309595157 1.9449591510659643 chr3 198022430 248856888 1.256710605965193 2.2614953366894035 chr4 191154276 145928077 0.7634047223719965 1.7128170588192375 chr5 180915260 227558058 1.2578157199121842 2.24046978979835 chr6 171115067 174294836 1.0185826359755918 2.1952174124613766 chr7 159138663 216983699 1.363488261805995 6.6966774750402065 chr8 146364022 194226317 1.3270086073475078 2.3953781577811215 chr9 141213431 90986026 0.6443156671124293 1.8155121786926847 chr10 135534747 37316450 0.2753275512441101 4.475902737328775 chr11 135006516 147897371 1.095483206158731 2.129081148147617 chr12 133851895 108552325 0.8109883315436065 1.8629904158141735 chr13 115169878 110862457 0.96259941336397 2.059977548423068 chr14 107349540 73089130 0.680851822932823 1.6648347378512824 chr15 102531392 56788628 0.5538657663011148 1.555756489143026 chr16 90354753 46448239 0.5140652534349798 1.4306591726306566 chr17 81195210 29202799 0.3596615982642326 1.191574357899823 chr18 78077248 72512434 0.9287268168058382 2.0690425586632664 chr19 59128983 41354550 0.6993955908221862 3.0083419152307824 chr20 63025520 78315642 1.2426020761113912 2.383720534660963 chr21 48129895 41352753 0.8591905924581801 1.9616333310941036 chr22 51304566 17341760 0.33801591850518725 1.0703213923231072 chrMT 16571 1367 0.08249351276326111 0.37386655033120836 chrX 155270560 144531871 0.9308388596009444 2.02881536985043 chrY 59373566 2260358 0.03807010682161149 0.6144404454353382