BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-42_S39_L005_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 = 17,152,034 number of mapped reads = 17,152,034 (100%) number of mapped paired reads (first in pair) = 8,576,017 number of mapped paired reads (second in pair) = 8,576,017 number of mapped paired reads (both in pair) = 17,152,034 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,460,543,909 bp number of sequenced bases = 1,457,366,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,912,255 duplication rate = 36.66% >>>>>>> Insert size mean insert size = 139.0293 std insert size = 90.2378 median insert size = 116 >>>>>>> Mapping quality mean mapping quality = 24.2309 >>>>>>> ACTG content number of A's = 556,883,612 bp (38.21%) number of C's = 172,807,661 bp (11.86%) number of T's = 555,694,134 bp (38.13%) number of G's = 171,980,716 bp (11.8%) number of N's = 103,761 bp (0.01%) GC percentage = 23.66% >>>>>>> Mismatches and indels general error rate = 0.1839 number of mismatches = 262,798,642 number of insertions = 1,725,123 mapped reads with insertion percentage = 8.8% number of deletions = 1,654,467 mapped reads with deletion percentage = 8.73% homopolymer indels = 49.02% >>>>>>> Coverage mean coverageData = 1.5499X std coverageData = 6.8682X There is a 35.74% of reference with a coverageData >= 1X There is a 24.58% of reference with a coverageData >= 2X There is a 16.63% of reference with a coverageData >= 3X There is a 12.71% of reference with a coverageData >= 4X There is a 9.6% of reference with a coverageData >= 5X There is a 7.66% of reference with a coverageData >= 6X There is a 6.05% of reference with a coverageData >= 7X There is a 4.94% of reference with a coverageData >= 8X There is a 4.01% of reference with a coverageData >= 9X There is a 3.33% of reference with a coverageData >= 10X There is a 2.76% of reference with a coverageData >= 11X There is a 2.32% of reference with a coverageData >= 12X There is a 1.96% of reference with a coverageData >= 13X There is a 1.67% of reference with a coverageData >= 14X There is a 1.43% of reference with a coverageData >= 15X There is a 1.24% of reference with a coverageData >= 16X There is a 1.08% of reference with a coverageData >= 17X There is a 0.95% of reference with a coverageData >= 18X There is a 0.83% of reference with a coverageData >= 19X There is a 0.74% of reference with a coverageData >= 20X There is a 0.66% of reference with a coverageData >= 21X There is a 0.59% of reference with a coverageData >= 22X There is a 0.54% of reference with a coverageData >= 23X There is a 0.49% of reference with a coverageData >= 24X There is a 0.44% of reference with a coverageData >= 25X There is a 0.41% of reference with a coverageData >= 26X There is a 0.38% of reference with a coverageData >= 27X There is a 0.35% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 148334339 1.654707237775367 4.862510196989762 PGA_scaffold2__36_contigs__length_69596280 69596280 117317183 1.6856818065563275 5.788182988250219 PGA_scaffold3__111_contigs__length_57743597 57743597 93866358 1.625571714903732 5.495330097733313 PGA_scaffold4__129_contigs__length_65288255 65288255 99768975 1.528130519034396 6.239151402244607 PGA_scaffold5__109_contigs__length_67248332 67248332 91025154 1.353567460974348 5.0150664118892445 PGA_scaffold6__104_contigs__length_61759565 61759565 88749564 1.4370173105979616 6.353971359994456 PGA_scaffold7__69_contigs__length_43120122 43120122 65885782 1.5279590813773671 4.907314783578694 PGA_scaffold8__63_contigs__length_61151155 61151155 96292386 1.574661770493133 5.548279965685454 PGA_scaffold9__45_contigs__length_38581958 38581958 65416209 1.6955129389752588 10.10872119524596 PGA_scaffold10__49_contigs__length_53961475 53961475 78947286 1.4630305416966456 4.580855786794897 PGA_scaffold11__79_contigs__length_51449921 51449921 70125807 1.362991538898573 5.5140476053725616 PGA_scaffold12__71_contigs__length_50438331 50438331 83433409 1.654166728871342 6.357645183791403 PGA_scaffold13__52_contigs__length_44396874 44396874 68442824 1.541613582974333 5.721169278167285 PGA_scaffold14__91_contigs__length_45393038 45393038 88154175 1.9420197211739827 16.311712017747745 PGA_scaffold15__101_contigs__length_47938513 47938513 60829679 1.2689104269880045 4.96303305144702 PGA_scaffold16__33_contigs__length_31980953 31980953 50944821 1.5929738241383864 9.231029234429176 PGA_scaffold17__51_contigs__length_34923512 34923512 54724207 1.5669731898670443 5.502130642005868 PGA_scaffold18__69_contigs__length_27737463 27737463 38285751 1.3802902954751124 7.149625599518254