BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-215_S31_L004_dedup.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-215_S31_L004_dedup.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 = 14,413,552 number of mapped reads = 14,413,552 (100%) number of mapped paired reads (first in pair) = 7,206,776 number of mapped paired reads (second in pair) = 7,206,776 number of mapped paired reads (both in pair) = 14,413,552 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,290,135,434 bp number of sequenced bases = 1,283,442,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,789,811 duplication rate = 26.97% >>>>>>> Insert size mean insert size = 165.002 std insert size = 96.6457 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 19.9774 >>>>>>> ACTG content number of A's = 488,485,381 bp (38.06%) number of C's = 155,196,944 bp (12.09%) number of T's = 486,587,859 bp (37.91%) number of G's = 153,172,621 bp (11.93%) number of N's = 80,905 bp (0.01%) GC percentage = 24.03% >>>>>>> Mismatches and indels general error rate = 0.2101 number of mismatches = 253,398,514 number of insertions = 5,086,046 mapped reads with insertion percentage = 21.04% number of deletions = 3,154,195 mapped reads with deletion percentage = 16.87% homopolymer indels = 40.16% >>>>>>> Coverage mean coverageData = 1.3691X std coverageData = 9.3638X There is a 35.06% of reference with a coverageData >= 1X There is a 22.64% of reference with a coverageData >= 2X There is a 14.43% of reference with a coverageData >= 3X There is a 10.44% of reference with a coverageData >= 4X There is a 7.53% of reference with a coverageData >= 5X There is a 5.77% of reference with a coverageData >= 6X There is a 4.43% of reference with a coverageData >= 7X There is a 3.54% of reference with a coverageData >= 8X There is a 2.83% of reference with a coverageData >= 9X There is a 2.34% of reference with a coverageData >= 10X There is a 1.93% of reference with a coverageData >= 11X There is a 1.64% of reference with a coverageData >= 12X There is a 1.39% of reference with a coverageData >= 13X There is a 1.21% of reference with a coverageData >= 14X There is a 1.05% of reference with a coverageData >= 15X There is a 0.93% of reference with a coverageData >= 16X There is a 0.83% of reference with a coverageData >= 17X There is a 0.74% of reference with a coverageData >= 18X There is a 0.67% of reference with a coverageData >= 19X There is a 0.61% of reference with a coverageData >= 20X There is a 0.55% of reference with a coverageData >= 21X There is a 0.51% of reference with a coverageData >= 22X There is a 0.47% of reference with a coverageData >= 23X There is a 0.43% of reference with a coverageData >= 24X There is a 0.4% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.35% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 126253204 1.408386566856444 5.036984254313136 PGA_scaffold2__36_contigs__length_69596280 69596280 100957133 1.4506110527746598 6.411789523335529 PGA_scaffold3__111_contigs__length_57743597 57743597 81097432 1.4044402533496485 5.318507904239403 PGA_scaffold4__129_contigs__length_65288255 65288255 87705726 1.3433614667753029 10.783680021767521 PGA_scaffold5__109_contigs__length_67248332 67248332 81602547 1.213450870424563 6.3993199175908835 PGA_scaffold6__104_contigs__length_61759565 61759565 79466626 1.2867096133206248 7.735199258338472 PGA_scaffold7__69_contigs__length_43120122 43120122 58049178 1.3462201707128751 4.953676775898408 PGA_scaffold8__63_contigs__length_61151155 61151155 83350288 1.36302066575848 5.255706233874089 PGA_scaffold9__45_contigs__length_38581958 38581958 60192393 1.5601176332212066 15.129824146176393 PGA_scaffold10__49_contigs__length_53961475 53961475 69329468 1.2847956435586685 5.2448060649545045 PGA_scaffold11__79_contigs__length_51449921 51449921 61086227 1.1872948648453707 5.7138105352030415 PGA_scaffold12__71_contigs__length_50438331 50438331 72440256 1.4362143743416094 7.594443612203301 PGA_scaffold13__52_contigs__length_44396874 44396874 60650462 1.366097577050132 6.572347127287084 PGA_scaffold14__91_contigs__length_45393038 45393038 79737267 1.7565968376031584 24.43969048268877 PGA_scaffold15__101_contigs__length_47938513 47938513 55103718 1.149466567726037 5.0456290765291225 PGA_scaffold16__33_contigs__length_31980953 31980953 47826600 1.495471382607016 17.80386397797246 PGA_scaffold17__51_contigs__length_34923512 34923512 49335579 1.4126751914297737 6.446652563756348 PGA_scaffold18__69_contigs__length_27737463 27737463 35951330 1.2961289934843716 9.120297359123274