BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-229_S36_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 = 12,072,532 number of mapped reads = 12,072,532 (100%) number of mapped paired reads (first in pair) = 6,036,266 number of mapped paired reads (second in pair) = 6,036,266 number of mapped paired reads (both in pair) = 12,072,532 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,043,744,887 bp number of sequenced bases = 1,041,433,079 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,252,177 duplication rate = 33.34% >>>>>>> Insert size mean insert size = 140.5859 std insert size = 89.435 median insert size = 117 >>>>>>> Mapping quality mean mapping quality = 24.0295 >>>>>>> ACTG content number of A's = 398,756,007 bp (38.29%) number of C's = 123,401,473 bp (11.85%) number of T's = 397,382,381 bp (38.16%) number of G's = 121,893,218 bp (11.7%) number of N's = 60,161 bp (0.01%) GC percentage = 23.55% >>>>>>> Mismatches and indels general error rate = 0.1863 number of mismatches = 190,068,974 number of insertions = 1,315,534 mapped reads with insertion percentage = 9.54% number of deletions = 1,228,641 mapped reads with deletion percentage = 9.22% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 1.1076X std coverageData = 7.6795X There is a 32.22% of reference with a coverageData >= 1X There is a 20.82% of reference with a coverageData >= 2X There is a 12.64% of reference with a coverageData >= 3X There is a 8.97% of reference with a coverageData >= 4X There is a 6.16% of reference with a coverageData >= 5X There is a 4.58% of reference with a coverageData >= 6X There is a 3.35% of reference with a coverageData >= 7X There is a 2.59% of reference with a coverageData >= 8X There is a 1.98% of reference with a coverageData >= 9X There is a 1.58% of reference with a coverageData >= 10X There is a 1.26% of reference with a coverageData >= 11X There is a 1.04% of reference with a coverageData >= 12X There is a 0.86% of reference with a coverageData >= 13X There is a 0.73% of reference with a coverageData >= 14X There is a 0.62% of reference with a coverageData >= 15X There is a 0.54% of reference with a coverageData >= 16X There is a 0.48% of reference with a coverageData >= 17X There is a 0.42% of reference with a coverageData >= 18X There is a 0.38% of reference with a coverageData >= 19X There is a 0.34% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 105495800 1.1768324515532615 4.017588523824772 PGA_scaffold2__36_contigs__length_69596280 69596280 84180499 1.2095545767676088 5.581061944536802 PGA_scaffold3__111_contigs__length_57743597 57743597 66414636 1.1501645108807474 3.9999281225479706 PGA_scaffold4__129_contigs__length_65288255 65288255 70786366 1.0842128649325977 5.822038652376056 PGA_scaffold5__109_contigs__length_67248332 67248332 64870036 0.964634126538633 4.247013012821793 PGA_scaffold6__104_contigs__length_61759565 61759565 64425901 1.0431728429434373 7.840903198721866 PGA_scaffold7__69_contigs__length_43120122 43120122 46051439 1.067980257569772 3.6912634972290763 PGA_scaffold8__63_contigs__length_61151155 61151155 67667744 1.106565264384622 4.312865678793845 PGA_scaffold9__45_contigs__length_38581958 38581958 47436423 1.2294975542713513 10.752683913066575 PGA_scaffold10__49_contigs__length_53961475 53961475 56475744 1.046593778246425 3.4571196730587563 PGA_scaffold11__79_contigs__length_51449921 51449921 49350951 0.9592036302640776 4.507338728386972 PGA_scaffold12__71_contigs__length_50438331 50438331 59370342 1.1770877589109758 5.244064037630861 PGA_scaffold13__52_contigs__length_44396874 44396874 48675244 1.0963664694050306 4.519520925939718 PGA_scaffold14__91_contigs__length_45393038 45393038 64529694 1.4215768946771088 21.380871343709618 PGA_scaffold15__101_contigs__length_47938513 47938513 42921783 0.89535073814242 3.7122647758412866 PGA_scaffold16__33_contigs__length_31980953 31980953 38398089 1.200654933578746 17.82161275164118 PGA_scaffold17__51_contigs__length_34923512 34923512 38816959 1.1114849789448438 4.7286783264676835 PGA_scaffold18__69_contigs__length_27737463 27737463 27877237 1.005039177519588 6.7967571197124075