BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-200_S25_L003_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 = 15,001,974 number of mapped reads = 15,001,974 (100%) number of mapped paired reads (first in pair) = 7,500,987 number of mapped paired reads (second in pair) = 7,500,987 number of mapped paired reads (both in pair) = 15,001,974 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,261,947,264 bp number of sequenced bases = 1,259,147,873 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,845,680 duplication rate = 37.06% >>>>>>> Insert size mean insert size = 134.8773 std insert size = 89.9467 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 24.1978 >>>>>>> ACTG content number of A's = 482,802,585 bp (38.34%) number of C's = 148,189,857 bp (11.77%) number of T's = 481,411,324 bp (38.23%) number of G's = 146,744,107 bp (11.65%) number of N's = 106,890 bp (0.01%) GC percentage = 23.42% >>>>>>> Mismatches and indels general error rate = 0.1851 number of mismatches = 228,387,172 number of insertions = 1,572,228 mapped reads with insertion percentage = 9.19% number of deletions = 1,468,556 mapped reads with deletion percentage = 8.87% homopolymer indels = 48.82% >>>>>>> Coverage mean coverageData = 1.3391X std coverageData = 7.3512X There is a 34.47% of reference with a coverageData >= 1X There is a 23.24% of reference with a coverageData >= 2X There is a 14.93% of reference with a coverageData >= 3X There is a 11.1% of reference with a coverageData >= 4X There is a 8.02% of reference with a coverageData >= 5X There is a 6.23% of reference with a coverageData >= 6X There is a 4.74% of reference with a coverageData >= 7X There is a 3.78% of reference with a coverageData >= 8X There is a 2.98% of reference with a coverageData >= 9X There is a 2.43% of reference with a coverageData >= 10X There is a 1.96% of reference with a coverageData >= 11X There is a 1.63% of reference with a coverageData >= 12X There is a 1.35% of reference with a coverageData >= 13X There is a 1.15% of reference with a coverageData >= 14X There is a 0.97% of reference with a coverageData >= 15X There is a 0.84% of reference with a coverageData >= 16X There is a 0.73% of reference with a coverageData >= 17X There is a 0.64% of reference with a coverageData >= 18X There is a 0.56% of reference with a coverageData >= 19X There is a 0.5% of reference with a coverageData >= 20X There is a 0.45% of reference with a coverageData >= 21X There is a 0.41% 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 0.17% 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 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% 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 0.1% 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 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 128949325 1.4384624815953646 4.3702909002839405 PGA_scaffold2__36_contigs__length_69596280 69596280 101964813 1.465089987568301 5.813178850299996 PGA_scaffold3__111_contigs__length_57743597 57743597 80559553 1.395125298481146 4.6310797889409 PGA_scaffold4__129_contigs__length_65288255 65288255 85414167 1.3082623666385325 6.297576861829585 PGA_scaffold5__109_contigs__length_67248332 67248332 78912341 1.1734468150079915 4.754815285556303 PGA_scaffold6__104_contigs__length_61759565 61759565 76623389 1.2406724205392314 6.080279923797193 PGA_scaffold7__69_contigs__length_43120122 43120122 57095504 1.3241034893175858 4.45714036309796 PGA_scaffold8__63_contigs__length_61151155 61151155 82168642 1.3436973022014056 4.646689174783782 PGA_scaffold9__45_contigs__length_38581958 38581958 57066876 1.4791078254763534 12.015586597993398 PGA_scaffold10__49_contigs__length_53961475 53961475 68854273 1.2759894535870266 4.114394556087035 PGA_scaffold11__79_contigs__length_51449921 51449921 59092658 1.1485471085562988 4.715454140318917 PGA_scaffold12__71_contigs__length_50438331 50438331 72147634 1.4304127945867202 6.097099690421848 PGA_scaffold13__52_contigs__length_44396874 44396874 59160509 1.3325377142543864 5.391606529430177 PGA_scaffold14__91_contigs__length_45393038 45393038 77233867 1.7014474113849793 21.12079466593948 PGA_scaffold15__101_contigs__length_47938513 47938513 52196617 1.0888242820548064 4.358635751967463 PGA_scaffold16__33_contigs__length_31980953 31980953 44880987 1.4033661535977366 10.010180024792865 PGA_scaffold17__51_contigs__length_34923512 34923512 46937466 1.3440076129800462 4.805192250941795 PGA_scaffold18__69_contigs__length_27737463 27737463 32688643 1.1785015450043141 6.212630713874752