BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-227_S35_L004_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 = 8,418,704 number of mapped reads = 8,418,704 (100%) number of mapped paired reads (first in pair) = 4,209,352 number of mapped paired reads (second in pair) = 4,209,352 number of mapped paired reads (both in pair) = 8,418,704 number of mapped paired reads (singletons) = 0 number of mapped bases = 728,167,484 bp number of sequenced bases = 726,538,351 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,718,532 duplication rate = 31.43% >>>>>>> Insert size mean insert size = 144.7034 std insert size = 93.64 median insert size = 119 >>>>>>> Mapping quality mean mapping quality = 24.2119 >>>>>>> ACTG content number of A's = 278,921,142 bp (38.39%) number of C's = 85,246,184 bp (11.73%) number of T's = 278,070,134 bp (38.27%) number of G's = 84,300,891 bp (11.6%) number of N's = 42,240 bp (0.01%) GC percentage = 23.34% >>>>>>> Mismatches and indels general error rate = 0.1873 number of mismatches = 133,370,064 number of insertions = 914,141 mapped reads with insertion percentage = 9.49% number of deletions = 863,100 mapped reads with deletion percentage = 9.27% homopolymer indels = 49.48% >>>>>>> Coverage mean coverageData = 0.7727X std coverageData = 5.4738X There is a 26.66% of reference with a coverageData >= 1X There is a 16.05% of reference with a coverageData >= 2X There is a 8.83% of reference with a coverageData >= 3X There is a 5.93% of reference with a coverageData >= 4X There is a 3.79% of reference with a coverageData >= 5X There is a 2.69% of reference with a coverageData >= 6X There is a 1.87% of reference with a coverageData >= 7X There is a 1.39% of reference with a coverageData >= 8X There is a 1.03% of reference with a coverageData >= 9X There is a 0.81% of reference with a coverageData >= 10X There is a 0.64% of reference with a coverageData >= 11X There is a 0.52% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.37% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.13% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.1% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% 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 PGA_scaffold1__77_contigs__length_89643857 89643857 73336531 0.8180876353858804 2.6514719730719065 PGA_scaffold2__36_contigs__length_69596280 69596280 58064582 0.8343058278402237 3.896534210001445 PGA_scaffold3__111_contigs__length_57743597 57743597 46277468 0.8014302953797631 2.87791083411986 PGA_scaffold4__129_contigs__length_65288255 65288255 49546463 0.7588878428440153 4.346610730496614 PGA_scaffold5__109_contigs__length_67248332 67248332 45002917 0.6692049551504118 2.973626332657415 PGA_scaffold6__104_contigs__length_61759565 61759565 44992123 0.7285045320510273 4.2312931253826775 PGA_scaffold7__69_contigs__length_43120122 43120122 32256930 0.7480713992414029 2.5829749153171497 PGA_scaffold8__63_contigs__length_61151155 61151155 47481491 0.776461066025654 2.996362658094143 PGA_scaffold9__45_contigs__length_38581958 38581958 33264590 0.8621799339473647 8.18762799163954 PGA_scaffold10__49_contigs__length_53961475 53961475 39185704 0.7261792602963503 2.4641591539248693 PGA_scaffold11__79_contigs__length_51449921 51449921 35009654 0.6804607921555409 3.356418690209129 PGA_scaffold12__71_contigs__length_50438331 50438331 41397767 0.8207600485432399 3.848369654344723 PGA_scaffold13__52_contigs__length_44396874 44396874 33914498 0.7638938272996427 3.116289063518841 PGA_scaffold14__91_contigs__length_45393038 45393038 45799938 1.0089639296669237 17.29735045468039 PGA_scaffold15__101_contigs__length_47938513 47938513 29981520 0.625416145052309 2.6709571981808096 PGA_scaffold16__33_contigs__length_31980953 31980953 26557154 0.8304053353256858 9.396619721886616 PGA_scaffold17__51_contigs__length_34923512 34923512 27052361 0.774617426792586 2.965845476392681 PGA_scaffold18__69_contigs__length_27737463 27737463 19045793 0.6866450980033755 4.521021646135069