BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-209_S29_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 = 17,891,018 number of mapped reads = 17,891,018 (100%) number of mapped paired reads (first in pair) = 8,945,509 number of mapped paired reads (second in pair) = 8,945,509 number of mapped paired reads (both in pair) = 17,891,018 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,559,502,696 bp number of sequenced bases = 1,556,034,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,811,589 duplication rate = 33.99% >>>>>>> Insert size mean insert size = 143.4648 std insert size = 90.4653 median insert size = 119 >>>>>>> Mapping quality mean mapping quality = 24.4109 >>>>>>> ACTG content number of A's = 597,891,806 bp (38.42%) number of C's = 181,787,529 bp (11.68%) number of T's = 596,143,346 bp (38.31%) number of G's = 180,211,645 bp (11.58%) number of N's = 91,358 bp (0.01%) GC percentage = 23.26% >>>>>>> Mismatches and indels general error rate = 0.1854 number of mismatches = 282,693,427 number of insertions = 1,912,017 mapped reads with insertion percentage = 9.33% number of deletions = 1,828,229 mapped reads with deletion percentage = 9.24% homopolymer indels = 49.64% >>>>>>> Coverage mean coverageData = 1.6549X std coverageData = 9.8777X There is a 39.16% of reference with a coverageData >= 1X There is a 26.94% of reference with a coverageData >= 2X There is a 18.15% of reference with a coverageData >= 3X There is a 13.63% of reference with a coverageData >= 4X There is a 10.16% of reference with a coverageData >= 5X There is a 7.97% of reference with a coverageData >= 6X There is a 6.22% of reference with a coverageData >= 7X There is a 5% of reference with a coverageData >= 8X There is a 4.02% of reference with a coverageData >= 9X There is a 3.3% of reference with a coverageData >= 10X There is a 2.71% of reference with a coverageData >= 11X There is a 2.27% of reference with a coverageData >= 12X There is a 1.91% of reference with a coverageData >= 13X There is a 1.62% of reference with a coverageData >= 14X There is a 1.39% of reference with a coverageData >= 15X There is a 1.2% of reference with a coverageData >= 16X There is a 1.04% of reference with a coverageData >= 17X There is a 0.92% of reference with a coverageData >= 18X There is a 0.81% of reference with a coverageData >= 19X There is a 0.72% of reference with a coverageData >= 20X There is a 0.64% of reference with a coverageData >= 21X There is a 0.58% of reference with a coverageData >= 22X There is a 0.53% of reference with a coverageData >= 23X There is a 0.48% 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 0.29% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 158546193 1.7686230635970963 5.598546255771563 PGA_scaffold2__36_contigs__length_69596280 69596280 125767694 1.807103684277378 7.427689383887183 PGA_scaffold3__111_contigs__length_57743597 57743597 99553658 1.7240640204661999 5.484351115180203 PGA_scaffold4__129_contigs__length_65288255 65288255 105736931 1.6195398544500845 7.847322999983837 PGA_scaffold5__109_contigs__length_67248332 67248332 96586650 1.4362683374808463 5.70882625302635 PGA_scaffold6__104_contigs__length_61759565 61759565 95502558 1.5463606001758594 10.10861508061848 PGA_scaffold7__69_contigs__length_43120122 43120122 69693650 1.616267458612478 5.03664370721446 PGA_scaffold8__63_contigs__length_61151155 61151155 101695159 1.663012889944597 5.737577712165825 PGA_scaffold9__45_contigs__length_38581958 38581958 70936155 1.838583593917136 14.208314276025055 PGA_scaffold10__49_contigs__length_53961475 53961475 84313143 1.5624692060400498 4.752140003145834 PGA_scaffold11__79_contigs__length_51449921 51449921 74163723 1.4414739917676453 6.256426491786322 PGA_scaffold12__71_contigs__length_50438331 50438331 88389622 1.752429556005729 6.853713048697305 PGA_scaffold13__52_contigs__length_44396874 44396874 73294725 1.6508983267605732 6.2458547743917805 PGA_scaffold14__91_contigs__length_45393038 45393038 95233626 2.0979786812242 26.459724309732998 PGA_scaffold15__101_contigs__length_47938513 47938513 64606599 1.3476971845163408 5.2421278036189225 PGA_scaffold16__33_contigs__length_31980953 31980953 56313646 1.7608495281550867 22.339727339346776 PGA_scaffold17__51_contigs__length_34923512 34923512 58263635 1.6683211871704082 6.618000102649233 PGA_scaffold18__69_contigs__length_27737463 27737463 40905329 1.4747321699897356 8.88939710507024