BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-103_S27_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 = 15,671,672 number of mapped reads = 15,671,672 (100%) number of mapped paired reads (first in pair) = 7,835,836 number of mapped paired reads (second in pair) = 7,835,836 number of mapped paired reads (both in pair) = 15,671,672 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,465,375,230 bp number of sequenced bases = 1,462,207,011 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,533,872 duplication rate = 24.4% >>>>>>> Insert size mean insert size = 166.0608 std insert size = 88.5159 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 24.5284 >>>>>>> ACTG content number of A's = 567,981,952 bp (38.84%) number of C's = 164,384,034 bp (11.24%) number of T's = 566,574,626 bp (38.75%) number of G's = 163,266,399 bp (11.17%) number of N's = 19,125 bp (0%) GC percentage = 22.41% >>>>>>> Mismatches and indels general error rate = 0.1892 number of mismatches = 271,630,273 number of insertions = 1,671,547 mapped reads with insertion percentage = 9.31% number of deletions = 1,698,059 mapped reads with deletion percentage = 9.8% homopolymer indels = 51.42% >>>>>>> Coverage mean coverageData = 1.555X std coverageData = 8.0501X There is a 42.32% of reference with a coverageData >= 1X There is a 28.28% of reference with a coverageData >= 2X There is a 18.71% of reference with a coverageData >= 3X There is a 13.31% of reference with a coverageData >= 4X There is a 9.41% of reference with a coverageData >= 5X There is a 6.95% of reference with a coverageData >= 6X There is a 5.13% of reference with a coverageData >= 7X There is a 3.92% of reference with a coverageData >= 8X There is a 3.01% of reference with a coverageData >= 9X There is a 2.39% of reference with a coverageData >= 10X There is a 1.9% of reference with a coverageData >= 11X There is a 1.56% of reference with a coverageData >= 12X There is a 1.29% of reference with a coverageData >= 13X There is a 1.09% of reference with a coverageData >= 14X There is a 0.93% of reference with a coverageData >= 15X There is a 0.8% of reference with a coverageData >= 16X There is a 0.7% of reference with a coverageData >= 17X There is a 0.62% of reference with a coverageData >= 18X There is a 0.55% 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 0.38% of reference with a coverageData >= 23X There is a 0.35% of reference with a coverageData >= 24X There is a 0.32% of reference with a coverageData >= 25X There is a 0.3% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% 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 0.1% 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 148172792 1.6529051399472916 4.35323013101037 PGA_scaffold2__36_contigs__length_69596280 69596280 117195488 1.6839332217181724 6.173591514214752 PGA_scaffold3__111_contigs__length_57743597 57743597 93650388 1.621831559956336 4.840763267933937 PGA_scaffold4__129_contigs__length_65288255 65288255 102605659 1.5715791301207238 7.118055027641033 PGA_scaffold5__109_contigs__length_67248332 67248332 91615846 1.3623512030008418 5.012519260613605 PGA_scaffold6__104_contigs__length_61759565 61759565 90101738 1.4589114738745326 6.623811678882179 PGA_scaffold7__69_contigs__length_43120122 43120122 65251675 1.5132534875481103 4.501868899088397 PGA_scaffold8__63_contigs__length_61151155 61151155 95584669 1.5630885303801703 5.494740504533482 PGA_scaffold9__45_contigs__length_38581958 38581958 66150998 1.7145578251886542 13.04179706944005 PGA_scaffold10__49_contigs__length_53961475 53961475 77182693 1.4303295638230793 3.872644792534111 PGA_scaffold11__79_contigs__length_51449921 51449921 71505968 1.3898168667741977 5.4802259132855475 PGA_scaffold12__71_contigs__length_50438331 50438331 82979589 1.6451692067289063 6.116631491822315 PGA_scaffold13__52_contigs__length_44396874 44396874 66952845 1.5080531345517705 5.101321406618573 PGA_scaffold14__91_contigs__length_45393038 45393038 89507425 1.9718315614830626 23.906321535724494 PGA_scaffold15__101_contigs__length_47938513 47938513 62098291 1.2953737426106646 4.573091891733026 PGA_scaffold16__33_contigs__length_31980953 31980953 52144119 1.630474207569737 11.01448288214434 PGA_scaffold17__51_contigs__length_34923512 34923512 54339674 1.5559624702120451 4.695337924755612 PGA_scaffold18__69_contigs__length_27737463 27737463 38335373 1.3820792838912483 7.004309856135402