BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-206_S27_L004_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 = 13,475,352 number of mapped reads = 13,475,352 (100%) number of mapped paired reads (first in pair) = 6,737,676 number of mapped paired reads (second in pair) = 6,737,676 number of mapped paired reads (both in pair) = 13,475,352 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,123,891,099 bp number of sequenced bases = 1,121,468,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,097,751 duplication rate = 36.79% >>>>>>> Insert size mean insert size = 132.9713 std insert size = 89.3591 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 24.279 >>>>>>> ACTG content number of A's = 428,382,900 bp (38.2%) number of C's = 133,916,068 bp (11.94%) number of T's = 426,861,808 bp (38.06%) number of G's = 132,307,973 bp (11.8%) number of N's = 65,146 bp (0.01%) GC percentage = 23.74% >>>>>>> Mismatches and indels general error rate = 0.1863 number of mismatches = 204,809,762 number of insertions = 1,369,600 mapped reads with insertion percentage = 8.9% number of deletions = 1,283,950 mapped reads with deletion percentage = 8.64% homopolymer indels = 48.9% >>>>>>> Coverage mean coverageData = 1.1926X std coverageData = 8.3493X There is a 32.83% of reference with a coverageData >= 1X There is a 21.74% of reference with a coverageData >= 2X There is a 13.47% of reference with a coverageData >= 3X There is a 9.78% of reference with a coverageData >= 4X There is a 6.85% of reference with a coverageData >= 5X There is a 5.19% of reference with a coverageData >= 6X There is a 3.86% of reference with a coverageData >= 7X There is a 3.01% of reference with a coverageData >= 8X There is a 2.33% of reference with a coverageData >= 9X There is a 1.88% of reference with a coverageData >= 10X There is a 1.5% of reference with a coverageData >= 11X There is a 1.24% of reference with a coverageData >= 12X There is a 1.03% of reference with a coverageData >= 13X There is a 0.87% of reference with a coverageData >= 14X There is a 0.74% of reference with a coverageData >= 15X There is a 0.64% of reference with a coverageData >= 16X There is a 0.56% of reference with a coverageData >= 17X There is a 0.5% of reference with a coverageData >= 18X There is a 0.44% of reference with a coverageData >= 19X There is a 0.4% of reference with a coverageData >= 20X There is a 0.36% of reference with a coverageData >= 21X There is a 0.33% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 114531375 1.277626586281311 4.6418314896412864 PGA_scaffold2__36_contigs__length_69596280 69596280 90959025 1.306952397455726 6.204914706803683 PGA_scaffold3__111_contigs__length_57743597 57743597 71245865 1.2338314324270447 4.169441545622487 PGA_scaffold4__129_contigs__length_65288255 65288255 76022416 1.1644118226164875 6.012885394687555 PGA_scaffold5__109_contigs__length_67248332 67248332 70193502 1.0437954356994312 4.478842412272126 PGA_scaffold6__104_contigs__length_61759565 61759565 68732130 1.1128985445412383 8.648280704692574 PGA_scaffold7__69_contigs__length_43120122 43120122 49383638 1.1452573812291162 3.983066874917559 PGA_scaffold8__63_contigs__length_61151155 61151155 73072722 1.1949524420266469 4.493923628600703 PGA_scaffold9__45_contigs__length_38581958 38581958 50898026 1.3192183247931586 11.24392777583293 PGA_scaffold10__49_contigs__length_53961475 53961475 61195826 1.1340651084871198 3.723141444564321 PGA_scaffold11__79_contigs__length_51449921 51449921 52151115 1.0136286701003876 4.889362738632392 PGA_scaffold12__71_contigs__length_50438331 50438331 64567815 1.2801338529619468 5.677702412914349 PGA_scaffold13__52_contigs__length_44396874 44396874 52434558 1.1810416652307547 4.979656216592053 PGA_scaffold14__91_contigs__length_45393038 45393038 70185697 1.5461775658196748 23.126381998056736 PGA_scaffold15__101_contigs__length_47938513 47938513 45923566 0.9579680955060079 4.046495730288499 PGA_scaffold16__33_contigs__length_31980953 31980953 41224710 1.289039447948909 19.950566443458086 PGA_scaffold17__51_contigs__length_34923512 34923512 41661560 1.192937296798787 5.273649391312444 PGA_scaffold18__69_contigs__length_27737463 27737463 29507553 1.0638158579968182 7.2779142144095745