BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-159_S6_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 = 9,288,530 number of mapped reads = 9,288,530 (100%) number of mapped paired reads (first in pair) = 4,644,265 number of mapped paired reads (second in pair) = 4,644,265 number of mapped paired reads (both in pair) = 9,288,530 number of mapped paired reads (singletons) = 0 number of mapped bases = 835,074,181 bp number of sequenced bases = 833,189,756 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,822,076 duplication rate = 27.89% >>>>>>> Insert size mean insert size = 150.3878 std insert size = 89.0141 median insert size = 127 >>>>>>> Mapping quality mean mapping quality = 24.026 >>>>>>> ACTG content number of A's = 320,846,819 bp (38.51%) number of C's = 96,732,340 bp (11.61%) number of T's = 319,858,085 bp (38.39%) number of G's = 95,752,512 bp (11.49%) number of N's = 44,656 bp (0.01%) GC percentage = 23.1% >>>>>>> Mismatches and indels general error rate = 0.1867 number of mismatches = 152,396,881 number of insertions = 1,056,290 mapped reads with insertion percentage = 9.9% number of deletions = 993,598 mapped reads with deletion percentage = 9.66% homopolymer indels = 49.23% >>>>>>> Coverage mean coverageData = 0.8862X std coverageData = 5.8505X There is a 29.32% of reference with a coverageData >= 1X There is a 17.93% of reference with a coverageData >= 2X There is a 10.19% of reference with a coverageData >= 3X There is a 6.9% of reference with a coverageData >= 4X There is a 4.49% of reference with a coverageData >= 5X There is a 3.23% of reference with a coverageData >= 6X There is a 2.27% of reference with a coverageData >= 7X There is a 1.72% of reference with a coverageData >= 8X There is a 1.29% of reference with a coverageData >= 9X There is a 1.02% of reference with a coverageData >= 10X There is a 0.81% of reference with a coverageData >= 11X There is a 0.66% of reference with a coverageData >= 12X There is a 0.55% of reference with a coverageData >= 13X There is a 0.47% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.17% of reference with a coverageData >= 23X There is a 0.16% of reference with a coverageData >= 24X There is a 0.15% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.05% 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 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 83755457 0.9343134019768917 3.04089589294132 PGA_scaffold2__36_contigs__length_69596280 69596280 66827450 0.9602158333750023 4.119500340205159 PGA_scaffold3__111_contigs__length_57743597 57743597 53165931 0.9207242666230162 3.218038947744797 PGA_scaffold4__129_contigs__length_65288255 65288255 56971376 0.8726129378094115 4.861984430411218 PGA_scaffold5__109_contigs__length_67248332 67248332 51983692 0.7730108755708618 3.3936131350246734 PGA_scaffold6__104_contigs__length_61759565 61759565 52033840 0.8425227735979034 5.295666503513466 PGA_scaffold7__69_contigs__length_43120122 43120122 37603231 0.8720576208017222 3.0599652550063556 PGA_scaffold8__63_contigs__length_61151155 61151155 54634710 0.8934370904359861 3.5264365069029044 PGA_scaffold9__45_contigs__length_38581958 38581958 37934061 0.9832072545410993 8.802678996877654 PGA_scaffold10__49_contigs__length_53961475 53961475 44932965 0.8326860042280164 2.7410081682434004 PGA_scaffold11__79_contigs__length_51449921 51449921 39864740 0.7748260682460523 3.4975982446997502 PGA_scaffold12__71_contigs__length_50438331 50438331 47355729 0.9388837430009331 4.78702644999453 PGA_scaffold13__52_contigs__length_44396874 44396874 38795878 0.8738425592756823 3.6628921153225287 PGA_scaffold14__91_contigs__length_45393038 45393038 51431925 1.1330355328938329 17.751548695798448 PGA_scaffold15__101_contigs__length_47938513 47938513 34855340 0.7270842965028974 3.122129939206642 PGA_scaffold16__33_contigs__length_31980953 31980953 29868927 0.9339598791818368 9.510634056189076 PGA_scaffold17__51_contigs__length_34923512 34923512 31170269 0.8925296230230224 3.3687471499551616 PGA_scaffold18__69_contigs__length_27737463 27737463 21888660 0.7891370598673715 4.60907297908791