BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-181_S16_L003_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 = 16,420,530 number of mapped reads = 16,420,530 (100%) number of mapped paired reads (first in pair) = 8,210,265 number of mapped paired reads (second in pair) = 8,210,265 number of mapped paired reads (both in pair) = 16,420,530 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,503,867,602 bp number of sequenced bases = 1,500,463,597 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,535,382 duplication rate = 28.03% >>>>>>> Insert size mean insert size = 159.0146 std insert size = 90.8537 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 24.3568 >>>>>>> ACTG content number of A's = 578,212,549 bp (38.54%) number of C's = 173,561,618 bp (11.57%) number of T's = 576,582,298 bp (38.43%) number of G's = 172,107,132 bp (11.47%) number of N's = 137,476 bp (0.01%) GC percentage = 23.04% >>>>>>> Mismatches and indels general error rate = 0.186 number of mismatches = 273,623,002 number of insertions = 1,802,138 mapped reads with insertion percentage = 9.55% number of deletions = 1,753,764 mapped reads with deletion percentage = 9.64% homopolymer indels = 50.1% >>>>>>> Coverage mean coverageData = 1.5959X std coverageData = 9.2641X There is a 39.63% of reference with a coverageData >= 1X There is a 26.67% of reference with a coverageData >= 2X There is a 17.9% of reference with a coverageData >= 3X There is a 13.18% of reference with a coverageData >= 4X There is a 9.71% of reference with a coverageData >= 5X There is a 7.47% of reference with a coverageData >= 6X There is a 5.76% of reference with a coverageData >= 7X There is a 4.56% of reference with a coverageData >= 8X There is a 3.62% of reference with a coverageData >= 9X There is a 2.94% of reference with a coverageData >= 10X There is a 2.4% of reference with a coverageData >= 11X There is a 1.99% of reference with a coverageData >= 12X There is a 1.66% of reference with a coverageData >= 13X There is a 1.41% of reference with a coverageData >= 14X There is a 1.21% of reference with a coverageData >= 15X There is a 1.04% of reference with a coverageData >= 16X There is a 0.91% of reference with a coverageData >= 17X There is a 0.8% of reference with a coverageData >= 18X There is a 0.71% of reference with a coverageData >= 19X There is a 0.63% of reference with a coverageData >= 20X There is a 0.57% of reference with a coverageData >= 21X There is a 0.52% of reference with a coverageData >= 22X There is a 0.47% of reference with a coverageData >= 23X There is a 0.43% of reference with a coverageData >= 24X There is a 0.4% of reference with a coverageData >= 25X There is a 0.37% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.3% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% 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 152871014 1.705315000000502 5.247564575907957 PGA_scaffold2__36_contigs__length_69596280 69596280 121320892 1.7432094359066317 6.866370346865996 PGA_scaffold3__111_contigs__length_57743597 57743597 95627995 1.6560796342493178 5.273802994000872 PGA_scaffold4__129_contigs__length_65288255 65288255 101681770 1.5574282081823139 7.525324304871512 PGA_scaffold5__109_contigs__length_67248332 67248332 93649126 1.3925865997687497 5.685125242711813 PGA_scaffold6__104_contigs__length_61759565 61759565 91403588 1.4799907998056658 9.116626833904519 PGA_scaffold7__69_contigs__length_43120122 43120122 67265434 1.559954630926137 5.011685056772376 PGA_scaffold8__63_contigs__length_61151155 61151155 98355807 1.6084047308673075 5.786793530526639 PGA_scaffold9__45_contigs__length_38581958 38581958 68196474 1.7675742117598074 13.783638682042644 PGA_scaffold10__49_contigs__length_53961475 53961475 81570728 1.511647485544085 4.6316847613277226 PGA_scaffold11__79_contigs__length_51449921 51449921 71100407 1.3819342307639306 5.845401784815135 PGA_scaffold12__71_contigs__length_50438331 50438331 85306165 1.6912963476130882 6.839893480544853 PGA_scaffold13__52_contigs__length_44396874 44396874 70576509 1.58967293508097 6.0799191407419855 PGA_scaffold14__91_contigs__length_45393038 45393038 92384075 2.0352036142634913 25.81365847790479 PGA_scaffold15__101_contigs__length_47938513 47938513 62507910 1.3039184173276297 5.076856691219004 PGA_scaffold16__33_contigs__length_31980953 31980953 54722982 1.711111673251263 18.254367469749106 PGA_scaffold17__51_contigs__length_34923512 34923512 55777543 1.5971344176381803 5.76780457384483 PGA_scaffold18__69_contigs__length_27737463 27737463 39549183 1.4258399551537932 8.08465260909374