BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-230_S37_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 = 14,564,888 number of mapped reads = 14,564,888 (100%) number of mapped paired reads (first in pair) = 7,282,444 number of mapped paired reads (second in pair) = 7,282,444 number of mapped paired reads (both in pair) = 14,564,888 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,237,961,007 bp number of sequenced bases = 1,235,179,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,377,488 duplication rate = 35.57% >>>>>>> Insert size mean insert size = 135.8295 std insert size = 88.6481 median insert size = 112 >>>>>>> Mapping quality mean mapping quality = 24.1291 >>>>>>> ACTG content number of A's = 475,293,216 bp (38.48%) number of C's = 143,424,532 bp (11.61%) number of T's = 474,137,672 bp (38.39%) number of G's = 142,323,731 bp (11.52%) number of N's = 73,402 bp (0.01%) GC percentage = 23.13% >>>>>>> Mismatches and indels general error rate = 0.1852 number of mismatches = 224,070,661 number of insertions = 1,582,029 mapped reads with insertion percentage = 9.5% number of deletions = 1,481,683 mapped reads with deletion percentage = 9.21% homopolymer indels = 49.33% >>>>>>> Coverage mean coverageData = 1.3137X std coverageData = 8.0112X There is a 35.79% of reference with a coverageData >= 1X There is a 24% of reference with a coverageData >= 2X There is a 15.17% of reference with a coverageData >= 3X There is a 11.05% of reference with a coverageData >= 4X There is a 7.77% of reference with a coverageData >= 5X There is a 5.88% of reference with a coverageData >= 6X There is a 4.36% of reference with a coverageData >= 7X There is a 3.39% of reference with a coverageData >= 8X There is a 2.61% of reference with a coverageData >= 9X There is a 2.09% of reference with a coverageData >= 10X There is a 1.67% of reference with a coverageData >= 11X There is a 1.37% of reference with a coverageData >= 12X There is a 1.13% of reference with a coverageData >= 13X There is a 0.95% of reference with a coverageData >= 14X There is a 0.8% of reference with a coverageData >= 15X There is a 0.69% of reference with a coverageData >= 16X There is a 0.6% of reference with a coverageData >= 17X There is a 0.53% 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 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.2% 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 0.15% 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 0.09% 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 0.08% 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 124609851 1.3900545466266585 4.429741966595247 PGA_scaffold2__36_contigs__length_69596280 69596280 99152483 1.4246807875363454 6.506512395446631 PGA_scaffold3__111_contigs__length_57743597 57743597 78775814 1.364234618082417 4.404875603821601 PGA_scaffold4__129_contigs__length_65288255 65288255 85038737 1.3025120214960562 6.292195917792881 PGA_scaffold5__109_contigs__length_67248332 67248332 76768200 1.1415628866452776 4.640949584263668 PGA_scaffold6__104_contigs__length_61759565 61759565 76378162 1.2367017481421703 7.2594046663274 PGA_scaffold7__69_contigs__length_43120122 43120122 55661427 1.2908457680152203 4.173025811500104 PGA_scaffold8__63_contigs__length_61151155 61151155 80410353 1.3149441412840035 4.496270217314743 PGA_scaffold9__45_contigs__length_38581958 38581958 56212037 1.456951381264787 11.57316072127538 PGA_scaffold10__49_contigs__length_53961475 53961475 66001661 1.2231255909887564 3.7238194818881363 PGA_scaffold11__79_contigs__length_51449921 51449921 60185243 1.1697830012217123 5.172897097433897 PGA_scaffold12__71_contigs__length_50438331 50438331 70186967 1.3915402355403077 5.835463543721751 PGA_scaffold13__52_contigs__length_44396874 44396874 57587381 1.2971044087473367 4.9967378184888265 PGA_scaffold14__91_contigs__length_45393038 45393038 75660751 1.6667919648823681 22.844470830594908 PGA_scaffold15__101_contigs__length_47938513 47938513 51981786 1.084342895658862 4.123783053107816 PGA_scaffold16__33_contigs__length_31980953 31980953 44933149 1.4049971869193516 16.161251236471234 PGA_scaffold17__51_contigs__length_34923512 34923512 46088930 1.3197106293318954 4.87831921809745 PGA_scaffold18__69_contigs__length_27737463 27737463 32328075 1.1655022306834624 7.4897112991165615