BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats/genome_results.txt >>>>>>> Reference number of bases = 942,353,201 bp number of contigs = 18 >>>>>>> Globals number of windows = 417 number of reads = 16,819,540 number of mapped reads = 16,819,540 (100%) number of mapped paired reads (first in pair) = 8,409,770 number of mapped paired reads (second in pair) = 8,409,770 number of mapped paired reads (both in pair) = 16,819,540 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,530,560,045 bp number of sequenced bases = 1,527,104,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,842,633 duplication rate = 29.29% >>>>>>> Insert size mean insert size = 154.537 std insert size = 89.5368 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 24.3637 >>>>>>> ACTG content number of A's = 590,301,082 bp (38.65%) number of C's = 174,627,551 bp (11.44%) number of T's = 588,805,638 bp (38.56%) number of G's = 173,370,424 bp (11.35%) number of N's = 83,158 bp (0.01%) GC percentage = 22.79% >>>>>>> Mismatches and indels general error rate = 0.185 number of mismatches = 276,886,375 number of insertions = 1,870,577 mapped reads with insertion percentage = 9.69% number of deletions = 1,805,622 mapped reads with deletion percentage = 9.69% homopolymer indels = 49.58% >>>>>>> Coverage mean coverageData = 1.6242X std coverageData = 8.1547X There is a 39.79% of reference with a coverageData >= 1X There is a 27.04% of reference with a coverageData >= 2X There is a 18.16% of reference with a coverageData >= 3X There is a 13.47% of reference with a coverageData >= 4X There is a 9.95% of reference with a coverageData >= 5X There is a 7.72% of reference with a coverageData >= 6X There is a 5.98% of reference with a coverageData >= 7X There is a 4.77% of reference with a coverageData >= 8X There is a 3.81% of reference with a coverageData >= 9X There is a 3.11% of reference with a coverageData >= 10X There is a 2.54% of reference with a coverageData >= 11X There is a 2.12% of reference with a coverageData >= 12X There is a 1.77% of reference with a coverageData >= 13X There is a 1.51% of reference with a coverageData >= 14X There is a 1.28% of reference with a coverageData >= 15X There is a 1.11% of reference with a coverageData >= 16X There is a 0.96% of reference with a coverageData >= 17X There is a 0.85% of reference with a coverageData >= 18X There is a 0.75% of reference with a coverageData >= 19X There is a 0.67% of reference with a coverageData >= 20X There is a 0.6% of reference with a coverageData >= 21X There is a 0.54% of reference with a coverageData >= 22X There is a 0.49% of reference with a coverageData >= 23X There is a 0.45% of reference with a coverageData >= 24X There is a 0.41% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.35% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 154450475 1.7229342887377102 4.910322138582399 PGA_scaffold2__36_contigs__length_69596280 69596280 122551411 1.760890251605402 6.281634978368664 PGA_scaffold3__111_contigs__length_57743597 57743597 97988729 1.6969626779571767 5.386358209063855 PGA_scaffold4__129_contigs__length_65288255 65288255 104587676 1.6019370712236067 7.166744103474976 PGA_scaffold5__109_contigs__length_67248332 67248332 95450741 1.4193770783786874 5.391508225149135 PGA_scaffold6__104_contigs__length_61759565 61759565 93473676 1.5135093001383673 7.4512417896610925 PGA_scaffold7__69_contigs__length_43120122 43120122 69396469 1.609375525421751 5.00405582419643 PGA_scaffold8__63_contigs__length_61151155 61151155 100514192 1.6437006300208066 5.505493876342513 PGA_scaffold9__45_contigs__length_38581958 38581958 69178967 1.7930393009084713 12.07541144952643 PGA_scaffold10__49_contigs__length_53961475 53961475 82680518 1.532213824770357 4.750647261670437 PGA_scaffold11__79_contigs__length_51449921 51449921 71761343 1.3947804312469207 5.266280467752335 PGA_scaffold12__71_contigs__length_50438331 50438331 87512788 1.7350452773704983 6.9193670154203835 PGA_scaffold13__52_contigs__length_44396874 44396874 72112296 1.6242651678584397 6.0277319902878155 PGA_scaffold14__91_contigs__length_45393038 45393038 93318157 2.055781263197233 22.894809244774805 PGA_scaffold15__101_contigs__length_47938513 47938513 64341649 1.3421703130424592 5.169710719862915 PGA_scaffold16__33_contigs__length_31980953 31980953 53906293 1.6855749420600443 11.904173988867736 PGA_scaffold17__51_contigs__length_34923512 34923512 57505222 1.6466047859104205 5.544927152499383 PGA_scaffold18__69_contigs__length_27737463 27737463 39829443 1.4359439794475797 7.1276081585808