BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-162_S9_L002_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 = 12,766,328 number of mapped reads = 12,766,328 (100%) number of mapped paired reads (first in pair) = 6,383,164 number of mapped paired reads (second in pair) = 6,383,164 number of mapped paired reads (both in pair) = 12,766,328 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,092,267,863 bp number of sequenced bases = 1,089,851,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,527,973 duplication rate = 34.88% >>>>>>> Insert size mean insert size = 133.2097 std insert size = 84.6501 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 23.9259 >>>>>>> ACTG content number of A's = 419,752,058 bp (38.51%) number of C's = 126,549,812 bp (11.61%) number of T's = 418,387,234 bp (38.39%) number of G's = 125,162,279 bp (11.48%) number of N's = 57,799 bp (0.01%) GC percentage = 23.1% >>>>>>> Mismatches and indels general error rate = 0.1874 number of mismatches = 200,092,350 number of insertions = 1,378,624 mapped reads with insertion percentage = 9.46% number of deletions = 1,292,281 mapped reads with deletion percentage = 9.17% homopolymer indels = 48.89% >>>>>>> Coverage mean coverageData = 1.1591X std coverageData = 7.9099X There is a 33.57% of reference with a coverageData >= 1X There is a 22.29% of reference with a coverageData >= 2X There is a 13.46% of reference with a coverageData >= 3X There is a 9.62% of reference with a coverageData >= 4X There is a 6.5% of reference with a coverageData >= 5X There is a 4.82% of reference with a coverageData >= 6X There is a 3.46% of reference with a coverageData >= 7X There is a 2.65% of reference with a coverageData >= 8X There is a 2% of reference with a coverageData >= 9X There is a 1.59% of reference with a coverageData >= 10X There is a 1.25% of reference with a coverageData >= 11X There is a 1.03% of reference with a coverageData >= 12X There is a 0.85% of reference with a coverageData >= 13X There is a 0.72% of reference with a coverageData >= 14X There is a 0.61% of reference with a coverageData >= 15X There is a 0.53% of reference with a coverageData >= 16X There is a 0.47% of reference with a coverageData >= 17X There is a 0.42% of reference with a coverageData >= 18X There is a 0.37% of reference with a coverageData >= 19X There is a 0.34% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.15% 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 0.13% 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 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% 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 109136338 1.217443577868364 4.176845863260651 PGA_scaffold2__36_contigs__length_69596280 69596280 87662321 1.2595834288844174 6.432401835103749 PGA_scaffold3__111_contigs__length_57743597 57743597 69539983 1.2042890746830337 4.252617295776869 PGA_scaffold4__129_contigs__length_65288255 65288255 75646074 1.158647508652207 6.3937917780609475 PGA_scaffold5__109_contigs__length_67248332 67248332 67922215 1.010020813601741 4.592326920908811 PGA_scaffold6__104_contigs__length_61759565 61759565 66958786 1.0841848707969364 6.435017543797549 PGA_scaffold7__69_contigs__length_43120122 43120122 49139449 1.1395943870474208 3.7281395143743645 PGA_scaffold8__63_contigs__length_61151155 61151155 70759284 1.1571209734305101 4.584643963513719 PGA_scaffold9__45_contigs__length_38581958 38581958 50287050 1.3033825292122292 12.004222959225155 PGA_scaffold10__49_contigs__length_53961475 53961475 57600431 1.0674361847966536 3.445582885989095 PGA_scaffold11__79_contigs__length_51449921 51449921 53172451 1.0334797404256462 4.8942082484933955 PGA_scaffold12__71_contigs__length_50438331 50438331 61890717 1.2270571958457548 5.560433114362563 PGA_scaffold13__52_contigs__length_44396874 44396874 50625491 1.1402940441257192 4.72859003584702 PGA_scaffold14__91_contigs__length_45393038 45393038 67254854 1.4816116515488564 24.311577895807407 PGA_scaffold15__101_contigs__length_47938513 47938513 46053394 0.9606763146783464 3.9310956753032262 PGA_scaffold16__33_contigs__length_31980953 31980953 39281077 1.2282647424546729 12.894570491731525 PGA_scaffold17__51_contigs__length_34923512 34923512 40929983 1.1719893176837426 4.446422205762133 PGA_scaffold18__69_contigs__length_27737463 27737463 28407965 1.0241731552737898 7.019103598733505