BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-151_S2_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 = 14,420,554 number of mapped reads = 14,420,554 (100%) number of mapped paired reads (first in pair) = 7,210,277 number of mapped paired reads (second in pair) = 7,210,277 number of mapped paired reads (both in pair) = 14,420,554 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,307,194,387 bp number of sequenced bases = 1,304,304,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,858,965 duplication rate = 28.88% >>>>>>> Insert size mean insert size = 152.0668 std insert size = 88.4144 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 23.9914 >>>>>>> ACTG content number of A's = 501,321,250 bp (38.44%) number of C's = 152,380,355 bp (11.68%) number of T's = 499,743,542 bp (38.31%) number of G's = 150,859,618 bp (11.57%) number of N's = 70,201 bp (0.01%) GC percentage = 23.25% >>>>>>> Mismatches and indels general error rate = 0.1858 number of mismatches = 237,427,615 number of insertions = 1,573,542 mapped reads with insertion percentage = 9.48% number of deletions = 1,500,935 mapped reads with deletion percentage = 9.39% homopolymer indels = 48.43% >>>>>>> Coverage mean coverageData = 1.3872X std coverageData = 8.3587X There is a 36.79% of reference with a coverageData >= 1X There is a 24.2% of reference with a coverageData >= 2X There is a 15.57% of reference with a coverageData >= 3X There is a 11.24% of reference with a coverageData >= 4X There is a 8.05% of reference with a coverageData >= 5X There is a 6.09% of reference with a coverageData >= 6X There is a 4.6% of reference with a coverageData >= 7X There is a 3.61% of reference with a coverageData >= 8X There is a 2.83% of reference with a coverageData >= 9X There is a 2.29% of reference with a coverageData >= 10X There is a 1.86% of reference with a coverageData >= 11X There is a 1.54% of reference with a coverageData >= 12X There is a 1.29% of reference with a coverageData >= 13X There is a 1.1% of reference with a coverageData >= 14X There is a 0.95% of reference with a coverageData >= 15X There is a 0.83% of reference with a coverageData >= 16X There is a 0.72% of reference with a coverageData >= 17X There is a 0.64% of reference with a coverageData >= 18X There is a 0.58% of reference with a coverageData >= 19X There is a 0.52% of reference with a coverageData >= 20X There is a 0.47% of reference with a coverageData >= 21X There is a 0.43% of reference with a coverageData >= 22X There is a 0.39% of reference with a coverageData >= 23X There is a 0.36% of reference with a coverageData >= 24X There is a 0.34% of reference with a coverageData >= 25X There is a 0.31% of reference with a coverageData >= 26X There is a 0.29% 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 0.24% 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 130849166 1.4596556906291973 4.686220784607224 PGA_scaffold2__36_contigs__length_69596280 69596280 105144492 1.5107774725890522 6.763131733354323 PGA_scaffold3__111_contigs__length_57743597 57743597 83587858 1.4475692949990628 4.987941964187217 PGA_scaffold4__129_contigs__length_65288255 65288255 89192710 1.3661371405928984 6.5844805198931935 PGA_scaffold5__109_contigs__length_67248332 67248332 81303967 1.2090109089992 5.099609715512415 PGA_scaffold6__104_contigs__length_61759565 61759565 80684110 1.3064228998374583 8.238485449355737 PGA_scaffold7__69_contigs__length_43120122 43120122 58443998 1.3553764527846188 4.628717258934441 PGA_scaffold8__63_contigs__length_61151155 61151155 85557000 1.399106852519793 5.504626750863408 PGA_scaffold9__45_contigs__length_38581958 38581958 59455436 1.541016554940006 11.728035720842831 PGA_scaffold10__49_contigs__length_53961475 53961475 69617181 1.2901274659375044 4.1966959490413505 PGA_scaffold11__79_contigs__length_51449921 51449921 61288257 1.1912215958504582 5.51014780384434 PGA_scaffold12__71_contigs__length_50438331 50438331 73912153 1.4653964858591375 6.023168698534082 PGA_scaffold13__52_contigs__length_44396874 44396874 61013881 1.3742832659794921 5.6891693161955805 PGA_scaffold14__91_contigs__length_45393038 45393038 80799265 1.7799924517059202 21.553844999745248 PGA_scaffold15__101_contigs__length_47938513 47938513 55015804 1.1476326768834069 4.731596644619542 PGA_scaffold16__33_contigs__length_31980953 31980953 47474018 1.4844466329693178 19.006861044858262 PGA_scaffold17__51_contigs__length_34923512 34923512 49327030 1.4124303993252454 5.670813801474187 PGA_scaffold18__69_contigs__length_27737463 27737463 34528061 1.2448168385118712 7.9660498697821644