BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-215_S31_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 = 12,785,804 number of mapped reads = 12,785,804 (100%) number of mapped paired reads (first in pair) = 6,392,902 number of mapped paired reads (second in pair) = 6,392,902 number of mapped paired reads (both in pair) = 12,785,804 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,083,613,036 bp number of sequenced bases = 1,081,238,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,781,668 duplication rate = 35.13% >>>>>>> Insert size mean insert size = 140.0071 std insert size = 93.1174 median insert size = 115 >>>>>>> Mapping quality mean mapping quality = 24.4351 >>>>>>> ACTG content number of A's = 414,121,407 bp (38.3%) number of C's = 127,735,140 bp (11.81%) number of T's = 412,877,616 bp (38.19%) number of G's = 126,504,300 bp (11.7%) number of N's = 61,448 bp (0.01%) GC percentage = 23.51% >>>>>>> Mismatches and indels general error rate = 0.1856 number of mismatches = 196,668,652 number of insertions = 1,325,090 mapped reads with insertion percentage = 9.08% number of deletions = 1,256,348 mapped reads with deletion percentage = 8.9% homopolymer indels = 49.13% >>>>>>> Coverage mean coverageData = 1.1499X std coverageData = 6.7645X There is a 32.01% of reference with a coverageData >= 1X There is a 20.79% of reference with a coverageData >= 2X There is a 12.93% of reference with a coverageData >= 3X There is a 9.38% of reference with a coverageData >= 4X There is a 6.65% of reference with a coverageData >= 5X There is a 5.08% of reference with a coverageData >= 6X There is a 3.82% of reference with a coverageData >= 7X There is a 3.01% of reference with a coverageData >= 8X There is a 2.35% of reference with a coverageData >= 9X There is a 1.9% of reference with a coverageData >= 10X There is a 1.53% of reference with a coverageData >= 11X There is a 1.27% of reference with a coverageData >= 12X There is a 1.05% of reference with a coverageData >= 13X There is a 0.89% of reference with a coverageData >= 14X There is a 0.75% of reference with a coverageData >= 15X There is a 0.65% of reference with a coverageData >= 16X There is a 0.56% of reference with a coverageData >= 17X There is a 0.49% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.39% of reference with a coverageData >= 20X There is a 0.35% of reference with a coverageData >= 21X There is a 0.32% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% 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 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 110189524 1.2291921352736976 3.889195897041503 PGA_scaffold2__36_contigs__length_69596280 69596280 87274381 1.2540092803810778 5.091260413714858 PGA_scaffold3__111_contigs__length_57743597 57743597 69335533 1.2007484223748652 4.013673656996521 PGA_scaffold4__129_contigs__length_65288255 65288255 73212908 1.1213794579132188 5.369834478347516 PGA_scaffold5__109_contigs__length_67248332 67248332 66999890 0.9963056035352669 4.133529103314306 PGA_scaffold6__104_contigs__length_61759565 61759565 65855979 1.066328414068331 6.292955813165421 PGA_scaffold7__69_contigs__length_43120122 43120122 48970777 1.1356827098030937 3.8397523387516928 PGA_scaffold8__63_contigs__length_61151155 61151155 70928376 1.1598861215295115 4.2000226859935825 PGA_scaffold9__45_contigs__length_38581958 38581958 49165940 1.2743246467688343 9.773195717583025 PGA_scaffold10__49_contigs__length_53961475 53961475 58841685 1.09043878063007 3.47004477727749 PGA_scaffold11__79_contigs__length_51449921 51449921 50844467 0.9882321685197534 4.207737912454694 PGA_scaffold12__71_contigs__length_50438331 50438331 61597858 1.221250917283524 5.492984892155584 PGA_scaffold13__52_contigs__length_44396874 44396874 50965082 1.1479430286015182 4.585931000894191 PGA_scaffold14__91_contigs__length_45393038 45393038 66561509 1.4663373929720236 19.428552805005655 PGA_scaffold15__101_contigs__length_47938513 47938513 45146715 0.9417629412076257 3.731333495123596 PGA_scaffold16__33_contigs__length_31980953 31980953 38709582 1.2103948872317845 12.03676525554721 PGA_scaffold17__51_contigs__length_34923512 34923512 40650300 1.1639808734012775 4.501105827550639 PGA_scaffold18__69_contigs__length_27737463 27737463 28362530 1.0225351179377868 5.947397489584694