BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-43_S40_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 = 12,841,222 number of mapped reads = 12,841,222 (100%) number of mapped paired reads (first in pair) = 6,420,611 number of mapped paired reads (second in pair) = 6,420,611 number of mapped paired reads (both in pair) = 12,841,222 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,093,718,890 bp number of sequenced bases = 1,091,312,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,619,682 duplication rate = 34.67% >>>>>>> Insert size mean insert size = 141.0786 std insert size = 92.5209 median insert size = 116 >>>>>>> Mapping quality mean mapping quality = 24.1267 >>>>>>> ACTG content number of A's = 419,039,444 bp (38.4%) number of C's = 127,759,759 bp (11.71%) number of T's = 417,753,360 bp (38.28%) number of G's = 126,759,997 bp (11.62%) number of N's = 77,717 bp (0.01%) GC percentage = 23.32% >>>>>>> Mismatches and indels general error rate = 0.186 number of mismatches = 199,162,373 number of insertions = 1,333,685 mapped reads with insertion percentage = 9.07% number of deletions = 1,261,677 mapped reads with deletion percentage = 8.88% homopolymer indels = 49.36% >>>>>>> Coverage mean coverageData = 1.1606X std coverageData = 6.1383X There is a 32.98% of reference with a coverageData >= 1X There is a 21.62% of reference with a coverageData >= 2X There is a 13.58% of reference with a coverageData >= 3X There is a 9.8% of reference with a coverageData >= 4X There is a 6.88% of reference with a coverageData >= 5X There is a 5.16% of reference with a coverageData >= 6X There is a 3.8% of reference with a coverageData >= 7X There is a 2.93% of reference with a coverageData >= 8X There is a 2.24% of reference with a coverageData >= 9X There is a 1.78% of reference with a coverageData >= 10X There is a 1.41% of reference with a coverageData >= 11X There is a 1.15% of reference with a coverageData >= 12X There is a 0.94% of reference with a coverageData >= 13X There is a 0.79% of reference with a coverageData >= 14X There is a 0.66% of reference with a coverageData >= 15X There is a 0.57% of reference with a coverageData >= 16X There is a 0.49% of reference with a coverageData >= 17X There is a 0.43% of reference with a coverageData >= 18X There is a 0.39% of reference with a coverageData >= 19X There is a 0.35% 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 0.2% 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 0.13% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% 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 0.08% 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 0.07% 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 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 110923737 1.2373824678248728 3.5818861683789747 PGA_scaffold2__36_contigs__length_69596280 69596280 88078763 1.265567110770863 4.785121484071017 PGA_scaffold3__111_contigs__length_57743597 57743597 70214937 1.215977885825159 3.958548782087611 PGA_scaffold4__129_contigs__length_65288255 65288255 75718880 1.159762655626192 5.167227530563107 PGA_scaffold5__109_contigs__length_67248332 67248332 67763682 1.0076633871008132 3.758237253013889 PGA_scaffold6__104_contigs__length_61759565 61759565 66467357 1.0762277389745216 5.112816141579181 PGA_scaffold7__69_contigs__length_43120122 43120122 49133874 1.1394650970607179 3.683053948416651 PGA_scaffold8__63_contigs__length_61151155 61151155 71407683 1.1677241909821654 4.0528532979587855 PGA_scaffold9__45_contigs__length_38581958 38581958 49236385 1.276150500189752 8.914151558272268 PGA_scaffold10__49_contigs__length_53961475 53961475 58763839 1.0889961588336865 3.4535218623477233 PGA_scaffold11__79_contigs__length_51449921 51449921 52502550 1.0204592928335108 4.270941888954753 PGA_scaffold12__71_contigs__length_50438331 50438331 62086635 1.2309415035957474 4.978476445088446 PGA_scaffold13__52_contigs__length_44396874 44396874 51164360 1.152431587863596 4.09530580188207 PGA_scaffold14__91_contigs__length_45393038 45393038 66848634 1.4726627021526957 17.73065229540095 PGA_scaffold15__101_contigs__length_47938513 47938513 45300185 0.9449643337914966 3.668914729122051 PGA_scaffold16__33_contigs__length_31980953 31980953 38773954 1.2124077103018163 9.6619868050302 PGA_scaffold17__51_contigs__length_34923512 34923512 41141867 1.1780564050946538 4.023372347645979 PGA_scaffold18__69_contigs__length_27737463 27737463 28191568 1.016371540540676 5.501668707201528