BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-199_S24_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 = 8,734,154 number of mapped reads = 8,734,154 (100%) number of mapped paired reads (first in pair) = 4,367,077 number of mapped paired reads (second in pair) = 4,367,077 number of mapped paired reads (both in pair) = 8,734,154 number of mapped paired reads (singletons) = 0 number of mapped bases = 752,099,245 bp number of sequenced bases = 750,376,085 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,915,751 duplication rate = 32.11% >>>>>>> Insert size mean insert size = 143.5568 std insert size = 93.4756 median insert size = 118 >>>>>>> Mapping quality mean mapping quality = 23.7657 >>>>>>> ACTG content number of A's = 287,199,805 bp (38.27%) number of C's = 88,890,522 bp (11.85%) number of T's = 286,296,166 bp (38.15%) number of G's = 87,989,592 bp (11.73%) number of N's = 64,551 bp (0.01%) GC percentage = 23.57% >>>>>>> Mismatches and indels general error rate = 0.1864 number of mismatches = 136,905,429 number of insertions = 995,928 mapped reads with insertion percentage = 10% number of deletions = 905,090 mapped reads with deletion percentage = 9.37% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.7981X std coverageData = 5.8196X There is a 26.69% of reference with a coverageData >= 1X There is a 16.16% of reference with a coverageData >= 2X There is a 9% of reference with a coverageData >= 3X There is a 6.13% of reference with a coverageData >= 4X There is a 3.99% of reference with a coverageData >= 5X There is a 2.88% of reference with a coverageData >= 6X There is a 2.04% of reference with a coverageData >= 7X There is a 1.55% of reference with a coverageData >= 8X There is a 1.16% of reference with a coverageData >= 9X There is a 0.92% of reference with a coverageData >= 10X There is a 0.73% of reference with a coverageData >= 11X There is a 0.6% of reference with a coverageData >= 12X There is a 0.49% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.15% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 75651478 0.8439114573126857 3.0296860217630104 PGA_scaffold2__36_contigs__length_69596280 69596280 60244764 0.8656319561907619 4.272126959227038 PGA_scaffold3__111_contigs__length_57743597 57743597 48178627 0.83435444799187 3.0281599655253055 PGA_scaffold4__129_contigs__length_65288255 65288255 51195912 0.7841519427958367 4.299456548101211 PGA_scaffold5__109_contigs__length_67248332 67248332 46635649 0.6934841000963414 3.209519539134719 PGA_scaffold6__104_contigs__length_61759565 61759565 46052049 0.7456666671794078 5.046837299899867 PGA_scaffold7__69_contigs__length_43120122 43120122 33695810 0.7814405070560793 2.769682780069849 PGA_scaffold8__63_contigs__length_61151155 61151155 49036164 0.8018845106032748 3.055028901200724 PGA_scaffold9__45_contigs__length_38581958 38581958 34317943 0.8894816328398886 8.044705298825397 PGA_scaffold10__49_contigs__length_53961475 53961475 40614623 0.7526596150309086 2.617408243967067 PGA_scaffold11__79_contigs__length_51449921 51449921 35599159 0.6919186328779786 3.39139135948235 PGA_scaffold12__71_contigs__length_50438331 50438331 42777756 0.8481199744694169 4.145125021062275 PGA_scaffold13__52_contigs__length_44396874 44396874 35326923 0.7957074410238884 3.392010788427691 PGA_scaffold14__91_contigs__length_45393038 45393038 46422132 1.0226707452363069 17.77831463013424 PGA_scaffold15__101_contigs__length_47938513 47938513 31261282 0.6521120502840795 2.7940526253804068 PGA_scaffold16__33_contigs__length_31980953 31980953 27435488 0.8578696200829288 11.588751293635509 PGA_scaffold17__51_contigs__length_34923512 34923512 28021956 0.8023808143923211 3.3519117144082045 PGA_scaffold18__69_contigs__length_27737463 27737463 19631530 0.707762278042516 4.905194042235041