BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-143_S37_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 = 15,792,158 number of mapped reads = 15,792,158 (100%) number of mapped paired reads (first in pair) = 7,896,079 number of mapped paired reads (second in pair) = 7,896,079 number of mapped paired reads (both in pair) = 15,792,158 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,453,750,443 bp number of sequenced bases = 1,450,609,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,898,191 duplication rate = 26.82% >>>>>>> Insert size mean insert size = 164.4114 std insert size = 92.1011 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 24.7913 >>>>>>> ACTG content number of A's = 563,597,708 bp (38.85%) number of C's = 163,079,204 bp (11.24%) number of T's = 562,092,875 bp (38.75%) number of G's = 161,840,067 bp (11.16%) number of N's = 18,851 bp (0%) GC percentage = 22.4% >>>>>>> Mismatches and indels general error rate = 0.187 number of mismatches = 266,529,247 number of insertions = 1,652,090 mapped reads with insertion percentage = 9.15% number of deletions = 1,682,344 mapped reads with deletion percentage = 9.64% homopolymer indels = 51.71% >>>>>>> Coverage mean coverageData = 1.5427X std coverageData = 6.8618X There is a 41.43% of reference with a coverageData >= 1X There is a 27.85% of reference with a coverageData >= 2X There is a 18.59% of reference with a coverageData >= 3X There is a 13.4% of reference with a coverageData >= 4X There is a 9.6% of reference with a coverageData >= 5X There is a 7.16% of reference with a coverageData >= 6X There is a 5.32% of reference with a coverageData >= 7X There is a 4.1% of reference with a coverageData >= 8X There is a 3.14% of reference with a coverageData >= 9X There is a 2.5% of reference with a coverageData >= 10X There is a 1.98% of reference with a coverageData >= 11X There is a 1.62% of reference with a coverageData >= 12X There is a 1.33% of reference with a coverageData >= 13X There is a 1.12% of reference with a coverageData >= 14X There is a 0.94% of reference with a coverageData >= 15X There is a 0.82% of reference with a coverageData >= 16X There is a 0.71% of reference with a coverageData >= 17X There is a 0.62% of reference with a coverageData >= 18X There is a 0.55% of reference with a coverageData >= 19X There is a 0.49% of reference with a coverageData >= 20X There is a 0.44% of reference with a coverageData >= 21X There is a 0.4% of reference with a coverageData >= 22X There is a 0.37% of reference with a coverageData >= 23X There is a 0.34% of reference with a coverageData >= 24X There is a 0.31% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 146360651 1.6326902466947624 4.086290517791137 PGA_scaffold2__36_contigs__length_69596280 69596280 116447567 1.6731866559534503 5.160340368606946 PGA_scaffold3__111_contigs__length_57743597 57743597 93493204 1.6191094572788738 4.725874164116515 PGA_scaffold4__129_contigs__length_65288255 65288255 100457098 1.5386702861027608 6.19876560474035 PGA_scaffold5__109_contigs__length_67248332 67248332 90254303 1.3421047082625037 4.5260854272731805 PGA_scaffold6__104_contigs__length_61759565 61759565 89050779 1.4418945308309734 5.696705537188221 PGA_scaffold7__69_contigs__length_43120122 43120122 65326708 1.5149935800274406 4.4023825228436175 PGA_scaffold8__63_contigs__length_61151155 61151155 95206149 1.556898622765179 5.077320552460768 PGA_scaffold9__45_contigs__length_38581958 38581958 65724963 1.703515487731338 11.13910477209987 PGA_scaffold10__49_contigs__length_53961475 53961475 77319821 1.4328707842029893 3.794800872887021 PGA_scaffold11__79_contigs__length_51449921 51449921 71304075 1.3858927985525964 5.016894527922714 PGA_scaffold12__71_contigs__length_50438331 50438331 82626649 1.6381717507662972 5.916790136178113 PGA_scaffold13__52_contigs__length_44396874 44396874 67545773 1.5214083090624804 5.082253940031935 PGA_scaffold14__91_contigs__length_45393038 45393038 87981398 1.9382134767009866 19.44210290094461 PGA_scaffold15__101_contigs__length_47938513 47938513 61894376 1.2911200645710474 4.309889989047682 PGA_scaffold16__33_contigs__length_31980953 31980953 51072527 1.5969670134595426 8.059744774713874 PGA_scaffold17__51_contigs__length_34923512 34923512 54256813 1.55358982796461 4.412910912132089 PGA_scaffold18__69_contigs__length_27737463 27737463 37427589 1.3493515610998743 5.465907758593457