BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-104_S28_L005_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 = 23,227,490 number of mapped reads = 23,227,490 (100%) number of mapped paired reads (first in pair) = 11,613,745 number of mapped paired reads (second in pair) = 11,613,745 number of mapped paired reads (both in pair) = 23,227,490 number of mapped paired reads (singletons) = 0 number of mapped bases = 2,129,827,627 bp number of sequenced bases = 2,125,239,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,889,216 duplication rate = 29.14% >>>>>>> Insert size mean insert size = 156.3397 std insert size = 86.5577 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 24.7599 >>>>>>> ACTG content number of A's = 825,956,145 bp (38.86%) number of C's = 238,322,603 bp (11.21%) number of T's = 824,035,289 bp (38.77%) number of G's = 236,925,468 bp (11.15%) number of N's = 28,643 bp (0%) GC percentage = 22.36% >>>>>>> Mismatches and indels general error rate = 0.1862 number of mismatches = 388,490,579 number of insertions = 2,448,292 mapped reads with insertion percentage = 9.21% number of deletions = 2,450,870 mapped reads with deletion percentage = 9.54% homopolymer indels = 51.01% >>>>>>> Coverage mean coverageData = 2.2601X std coverageData = 8.8666X There is a 48.59% of reference with a coverageData >= 1X There is a 35.6% of reference with a coverageData >= 2X There is a 25.87% of reference with a coverageData >= 3X There is a 19.89% of reference with a coverageData >= 4X There is a 15.2% of reference with a coverageData >= 5X There is a 11.95% of reference with a coverageData >= 6X There is a 9.35% of reference with a coverageData >= 7X There is a 7.48% of reference with a coverageData >= 8X There is a 5.97% of reference with a coverageData >= 9X There is a 4.86% of reference with a coverageData >= 10X There is a 3.95% of reference with a coverageData >= 11X There is a 3.28% of reference with a coverageData >= 12X There is a 2.72% of reference with a coverageData >= 13X There is a 2.3% of reference with a coverageData >= 14X There is a 1.94% of reference with a coverageData >= 15X There is a 1.67% of reference with a coverageData >= 16X There is a 1.44% of reference with a coverageData >= 17X There is a 1.26% of reference with a coverageData >= 18X There is a 1.11% of reference with a coverageData >= 19X There is a 0.98% of reference with a coverageData >= 20X There is a 0.88% of reference with a coverageData >= 21X There is a 0.79% of reference with a coverageData >= 22X There is a 0.71% of reference with a coverageData >= 23X There is a 0.65% of reference with a coverageData >= 24X There is a 0.6% of reference with a coverageData >= 25X There is a 0.55% of reference with a coverageData >= 26X There is a 0.51% of reference with a coverageData >= 27X There is a 0.47% of reference with a coverageData >= 28X There is a 0.44% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.38% of reference with a coverageData >= 31X There is a 0.36% of reference with a coverageData >= 32X There is a 0.34% of reference with a coverageData >= 33X There is a 0.32% of reference with a coverageData >= 34X There is a 0.3% of reference with a coverageData >= 35X There is a 0.29% of reference with a coverageData >= 36X There is a 0.27% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 216845195 2.4189632425119774 5.727924501249149 PGA_scaffold2__36_contigs__length_69596280 69596280 172945920 2.484987990737436 7.0462569329429385 PGA_scaffold3__111_contigs__length_57743597 57743597 137272775 2.3772813286986607 6.7582863517684695 PGA_scaffold4__129_contigs__length_65288255 65288255 147655249 2.261589760669817 8.717434607242732 PGA_scaffold5__109_contigs__length_67248332 67248332 133178555 1.9803993800173363 6.150038667652383 PGA_scaffold6__104_contigs__length_61759565 61759565 131191044 2.124222280386852 7.788157812545379 PGA_scaffold7__69_contigs__length_43120122 43120122 96119910 2.2291196207654513 6.22359446426049 PGA_scaffold8__63_contigs__length_61151155 61151155 139704667 2.284579367307126 6.723114894354282 PGA_scaffold9__45_contigs__length_38581958 38581958 95107763 2.4650838871370913 14.414623421481535 PGA_scaffold10__49_contigs__length_53961475 53961475 114491300 2.1217229514204345 5.410119955919282 PGA_scaffold11__79_contigs__length_51449921 51449921 101711036 1.9768939198176805 6.288245977188752 PGA_scaffold12__71_contigs__length_50438331 50438331 121752315 2.4138846901972233 8.034241681842216 PGA_scaffold13__52_contigs__length_44396874 44396874 98914436 2.227959473002536 7.235544685414077 PGA_scaffold14__91_contigs__length_45393038 45393038 126338581 2.783214928245164 22.95398944648861 PGA_scaffold15__101_contigs__length_47938513 47938513 89138309 1.8594299952524602 6.0601138039526115 PGA_scaffold16__33_contigs__length_31980953 31980953 74471271 2.3286132530196957 10.52908270497371 PGA_scaffold17__51_contigs__length_34923512 34923512 78574277 2.249896201733663 6.022800829897466 PGA_scaffold18__69_contigs__length_27737463 27737463 54415024 1.9617880698029233 7.646554843766123