BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-154_S5_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 = 13,539,046 number of mapped reads = 13,539,046 (100%) number of mapped paired reads (first in pair) = 6,769,523 number of mapped paired reads (second in pair) = 6,769,523 number of mapped paired reads (both in pair) = 13,539,046 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,222,325,505 bp number of sequenced bases = 1,219,547,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,452,332 duplication rate = 29.1% >>>>>>> Insert size mean insert size = 149.3384 std insert size = 87.4188 median insert size = 125 >>>>>>> Mapping quality mean mapping quality = 24.1212 >>>>>>> ACTG content number of A's = 471,192,707 bp (38.64%) number of C's = 139,985,651 bp (11.48%) number of T's = 469,692,468 bp (38.51%) number of G's = 138,677,151 bp (11.37%) number of N's = 65,360 bp (0.01%) GC percentage = 22.85% >>>>>>> Mismatches and indels general error rate = 0.1858 number of mismatches = 222,019,117 number of insertions = 1,538,696 mapped reads with insertion percentage = 9.92% number of deletions = 1,468,226 mapped reads with deletion percentage = 9.79% homopolymer indels = 49.4% >>>>>>> Coverage mean coverageData = 1.2971X std coverageData = 7.8308X There is a 36.14% of reference with a coverageData >= 1X There is a 23.72% of reference with a coverageData >= 2X There is a 14.97% of reference with a coverageData >= 3X There is a 10.71% of reference with a coverageData >= 4X There is a 7.53% of reference with a coverageData >= 5X There is a 5.63% of reference with a coverageData >= 6X There is a 4.19% of reference with a coverageData >= 7X There is a 3.24% of reference with a coverageData >= 8X There is a 2.5% of reference with a coverageData >= 9X There is a 2% of reference with a coverageData >= 10X There is a 1.6% of reference with a coverageData >= 11X There is a 1.32% of reference with a coverageData >= 12X There is a 1.09% of reference with a coverageData >= 13X There is a 0.92% of reference with a coverageData >= 14X There is a 0.78% of reference with a coverageData >= 15X There is a 0.68% of reference with a coverageData >= 16X There is a 0.59% of reference with a coverageData >= 17X There is a 0.52% of reference with a coverageData >= 18X There is a 0.47% of reference with a coverageData >= 19X There is a 0.42% of reference with a coverageData >= 20X There is a 0.38% of reference with a coverageData >= 21X There is a 0.35% of reference with a coverageData >= 22X There is a 0.32% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% 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 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 122960880 1.3716598561795483 4.166616027076922 PGA_scaffold2__36_contigs__length_69596280 69596280 99152062 1.4246747383624527 6.379516476936305 PGA_scaffold3__111_contigs__length_57743597 57743597 77989152 1.3506112547855307 4.434142616131939 PGA_scaffold4__129_contigs__length_65288255 65288255 82834850 1.2687557662553548 6.502841599784627 PGA_scaffold5__109_contigs__length_67248332 67248332 75756895 1.1265245210840322 4.601005886516805 PGA_scaffold6__104_contigs__length_61759565 61759565 75271262 1.2187790182783833 6.422041790804866 PGA_scaffold7__69_contigs__length_43120122 43120122 55209059 1.2803548886062985 4.081864508504043 PGA_scaffold8__63_contigs__length_61151155 61151155 79467010 1.2995177278335952 4.618693516655249 PGA_scaffold9__45_contigs__length_38581958 38581958 55927117 1.4495665823906605 11.688454326934503 PGA_scaffold10__49_contigs__length_53961475 53961475 65859743 1.2204956035764405 3.795262003560813 PGA_scaffold11__79_contigs__length_51449921 51449921 58548861 1.1379776656994285 5.13324502971425 PGA_scaffold12__71_contigs__length_50438331 50438331 69223995 1.3724481684376115 6.221549027818435 PGA_scaffold13__52_contigs__length_44396874 44396874 57128990 1.2867795602005674 5.08293924172257 PGA_scaffold14__91_contigs__length_45393038 45393038 73373929 1.6164137108426186 22.940532342033894 PGA_scaffold15__101_contigs__length_47938513 47938513 51261006 1.0693073854835673 4.236550687609605 PGA_scaffold16__33_contigs__length_31980953 31980953 44254503 1.3837768686880594 13.668880616676296 PGA_scaffold17__51_contigs__length_34923512 34923512 45463827 1.3018114272127042 4.589036675478509 PGA_scaffold18__69_contigs__length_27737463 27737463 32642364 1.176833079506947 7.427665377618435