BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-220_S32_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 = 8,724,714 number of mapped reads = 8,724,714 (100%) number of mapped paired reads (first in pair) = 4,362,357 number of mapped paired reads (second in pair) = 4,362,357 number of mapped paired reads (both in pair) = 8,724,714 number of mapped paired reads (singletons) = 0 number of mapped bases = 760,719,796 bp number of sequenced bases = 758,987,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,846,855 duplication rate = 31.22% >>>>>>> Insert size mean insert size = 145.1196 std insert size = 92.3272 median insert size = 119 >>>>>>> Mapping quality mean mapping quality = 23.8446 >>>>>>> ACTG content number of A's = 291,363,990 bp (38.39%) number of C's = 89,126,197 bp (11.74%) number of T's = 290,405,697 bp (38.26%) number of G's = 88,091,654 bp (11.61%) number of N's = 44,759 bp (0.01%) GC percentage = 23.35% >>>>>>> Mismatches and indels general error rate = 0.1878 number of mismatches = 139,561,065 number of insertions = 992,359 mapped reads with insertion percentage = 9.93% number of deletions = 918,369 mapped reads with deletion percentage = 9.51% homopolymer indels = 48.82% >>>>>>> Coverage mean coverageData = 0.8073X std coverageData = 5.9892X There is a 27.14% of reference with a coverageData >= 1X There is a 16.48% of reference with a coverageData >= 2X There is a 9.14% of reference with a coverageData >= 3X There is a 6.19% of reference with a coverageData >= 4X There is a 3.99% of reference with a coverageData >= 5X There is a 2.86% of reference with a coverageData >= 6X There is a 2.01% of reference with a coverageData >= 7X There is a 1.51% of reference with a coverageData >= 8X There is a 1.13% of reference with a coverageData >= 9X There is a 0.89% of reference with a coverageData >= 10X There is a 0.71% of reference with a coverageData >= 11X There is a 0.58% of reference with a coverageData >= 12X There is a 0.48% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.15% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.12% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 76418536 0.8524681841835521 3.010084060767697 PGA_scaffold2__36_contigs__length_69596280 69596280 61054930 0.8772728944707965 4.125392992543715 PGA_scaffold3__111_contigs__length_57743597 57743597 48464744 0.8393094042963759 3.0654794100653646 PGA_scaffold4__129_contigs__length_65288255 65288255 51833052 0.7939108190286293 4.634386617738939 PGA_scaffold5__109_contigs__length_67248332 67248332 47185233 0.7016565555856463 3.2174749759465344 PGA_scaffold6__104_contigs__length_61759565 61759565 47082271 0.7623478403709611 5.6795480217382766 PGA_scaffold7__69_contigs__length_43120122 43120122 33932384 0.7869269015519019 2.9074389800063236 PGA_scaffold8__63_contigs__length_61151155 61151155 49198685 0.8045422036591132 3.2467021791039268 PGA_scaffold9__45_contigs__length_38581958 38581958 35066239 0.9088766049664976 8.678028616575196 PGA_scaffold10__49_contigs__length_53961475 53961475 40562905 0.7517011905252775 2.539289630422161 PGA_scaffold11__79_contigs__length_51449921 51449921 36125731 0.7021532841615054 3.4640131157983376 PGA_scaffold12__71_contigs__length_50438331 50438331 43487937 0.8622001588434796 4.243406143862352 PGA_scaffold13__52_contigs__length_44396874 44396874 35458918 0.7986805107044248 3.400870530483828 PGA_scaffold14__91_contigs__length_45393038 45393038 47249997 1.0409084538470414 18.20655767381262 PGA_scaffold15__101_contigs__length_47938513 47938513 31385539 0.6547040580920814 2.876460569796621 PGA_scaffold16__33_contigs__length_31980953 31980953 27940426 0.8736583303192997 11.782100579387452 PGA_scaffold17__51_contigs__length_34923512 34923512 28289819 0.8100508047415163 3.491884823620048 PGA_scaffold18__69_contigs__length_27737463 27737463 19982450 0.7204137595424643 4.475377260902438