BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-208_S28_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 = 17,282,682 number of mapped reads = 17,282,682 (100%) number of mapped paired reads (first in pair) = 8,641,341 number of mapped paired reads (second in pair) = 8,641,341 number of mapped paired reads (both in pair) = 17,282,682 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,405,632,699 bp number of sequenced bases = 1,402,664,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,829,199 duplication rate = 39.81% >>>>>>> Insert size mean insert size = 125.8332 std insert size = 86.6137 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 24.3855 >>>>>>> ACTG content number of A's = 536,604,770 bp (38.26%) number of C's = 166,228,712 bp (11.85%) number of T's = 534,930,060 bp (38.14%) number of G's = 164,900,688 bp (11.76%) number of N's = 79,303 bp (0.01%) GC percentage = 23.61% >>>>>>> Mismatches and indels general error rate = 0.1885 number of mismatches = 259,463,988 number of insertions = 1,641,218 mapped reads with insertion percentage = 8.36% number of deletions = 1,585,291 mapped reads with deletion percentage = 8.34% homopolymer indels = 49.44% >>>>>>> Coverage mean coverageData = 1.4916X std coverageData = 9.1584X There is a 37.26% of reference with a coverageData >= 1X There is a 25.94% of reference with a coverageData >= 2X There is a 16.91% of reference with a coverageData >= 3X There is a 12.65% of reference with a coverageData >= 4X There is a 9.1% of reference with a coverageData >= 5X There is a 7.03% of reference with a coverageData >= 6X There is a 5.3% of reference with a coverageData >= 7X There is a 4.2% of reference with a coverageData >= 8X There is a 3.28% of reference with a coverageData >= 9X There is a 2.66% of reference with a coverageData >= 10X There is a 2.14% of reference with a coverageData >= 11X There is a 1.77% of reference with a coverageData >= 12X There is a 1.46% of reference with a coverageData >= 13X There is a 1.24% of reference with a coverageData >= 14X There is a 1.05% of reference with a coverageData >= 15X There is a 0.91% of reference with a coverageData >= 16X There is a 0.79% of reference with a coverageData >= 17X There is a 0.7% of reference with a coverageData >= 18X There is a 0.62% of reference with a coverageData >= 19X There is a 0.55% of reference with a coverageData >= 20X There is a 0.5% of reference with a coverageData >= 21X There is a 0.45% of reference with a coverageData >= 22X There is a 0.41% of reference with a coverageData >= 23X There is a 0.38% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.3% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 142546415 1.5901414750594678 5.02467443958462 PGA_scaffold2__36_contigs__length_69596280 69596280 112991649 1.6235300076383392 7.387366139215939 PGA_scaffold3__111_contigs__length_57743597 57743597 89037978 1.5419541321611814 5.080200939004282 PGA_scaffold4__129_contigs__length_65288255 65288255 97386344 1.4916364972536025 7.587339780706515 PGA_scaffold5__109_contigs__length_67248332 67248332 87675890 1.303763043520544 5.661926879017542 PGA_scaffold6__104_contigs__length_61759565 61759565 85222422 1.379906448499111 7.493262028234688 PGA_scaffold7__69_contigs__length_43120122 43120122 62800335 1.4564043905070585 4.8467889987888535 PGA_scaffold8__63_contigs__length_61151155 61151155 91131920 1.4902730782435754 5.472182294409824 PGA_scaffold9__45_contigs__length_38581958 38581958 63637936 1.6494221470045662 13.919070519412001 PGA_scaffold10__49_contigs__length_53961475 53961475 74988020 1.3896584554073068 4.254791670091991 PGA_scaffold11__79_contigs__length_51449921 51449921 67983185 1.3213467324857506 5.941565296247852 PGA_scaffold12__71_contigs__length_50438331 50438331 79394903 1.5740985362897912 6.801805608395331 PGA_scaffold13__52_contigs__length_44396874 44396874 65184293 1.468218077696191 6.04270840273374 PGA_scaffold14__91_contigs__length_45393038 45393038 86710026 1.9102053931706444 27.630011899865178 PGA_scaffold15__101_contigs__length_47938513 47938513 58145721 1.212922916486792 4.693961412094994 PGA_scaffold16__33_contigs__length_31980953 31980953 50756538 1.587086476128463 14.315616692370863 PGA_scaffold17__51_contigs__length_34923512 34923512 52216041 1.4951543533193339 5.2162866243423185 PGA_scaffold18__69_contigs__length_27737463 27737463 37823083 1.363610038884955 8.06621621338619