BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-220_S32_L004_dedup.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-220_S32_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 = 10,406,202 number of mapped reads = 10,406,202 (100%) number of mapped paired reads (first in pair) = 5,203,101 number of mapped paired reads (second in pair) = 5,203,101 number of mapped paired reads (both in pair) = 10,406,202 number of mapped paired reads (singletons) = 0 number of mapped bases = 942,629,434 bp number of sequenced bases = 937,487,580 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,122,494 duplication rate = 25.06% >>>>>>> Insert size mean insert size = 164.1957 std insert size = 95.7663 median insert size = 132 >>>>>>> Mapping quality mean mapping quality = 19.3246 >>>>>>> ACTG content number of A's = 356,201,067 bp (38%) number of C's = 114,208,645 bp (12.18%) number of T's = 354,666,646 bp (37.83%) number of G's = 112,411,222 bp (11.99%) number of N's = 60,093 bp (0.01%) GC percentage = 24.17% >>>>>>> Mismatches and indels general error rate = 0.2148 number of mismatches = 188,519,644 number of insertions = 4,082,483 mapped reads with insertion percentage = 22.72% number of deletions = 2,468,319 mapped reads with deletion percentage = 17.95% homopolymer indels = 39.14% >>>>>>> Coverage mean coverageData = 1.0003X std coverageData = 8.4696X There is a 30.13% of reference with a coverageData >= 1X There is a 18.33% of reference with a coverageData >= 2X There is a 10.58% of reference with a coverageData >= 3X There is a 7.24% of reference with a coverageData >= 4X There is a 4.86% of reference with a coverageData >= 5X There is a 3.57% of reference with a coverageData >= 6X There is a 2.63% of reference with a coverageData >= 7X There is a 2.05% of reference with a coverageData >= 8X There is a 1.61% of reference with a coverageData >= 9X There is a 1.31% of reference with a coverageData >= 10X There is a 1.08% of reference with a coverageData >= 11X There is a 0.92% of reference with a coverageData >= 12X There is a 0.79% of reference with a coverageData >= 13X There is a 0.69% of reference with a coverageData >= 14X There is a 0.6% of reference with a coverageData >= 15X There is a 0.54% of reference with a coverageData >= 16X There is a 0.48% of reference with a coverageData >= 17X There is a 0.44% of reference with a coverageData >= 18X There is a 0.4% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.23% 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 0.2% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% 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 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% 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 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.1% 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 0.09% 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 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 90772537 1.0125907121555469 4.220959063647581 PGA_scaffold2__36_contigs__length_69596280 69596280 73247137 1.0524576457247428 5.259293392352748 PGA_scaffold3__111_contigs__length_57743597 57743597 58929030 1.020529254524965 4.237712049579304 PGA_scaffold4__129_contigs__length_65288255 65288255 64656159 0.9903183811544665 10.278317253127161 PGA_scaffold5__109_contigs__length_67248332 67248332 59906055 0.8908184518242028 5.24133957927125 PGA_scaffold6__104_contigs__length_61759565 61759565 58670631 0.9499845246643172 6.960360579670406 PGA_scaffold7__69_contigs__length_43120122 43120122 41984159 0.9736558491184232 4.044181940598813 PGA_scaffold8__63_contigs__length_61151155 61151155 60033092 0.9817164042118256 4.173400081133774 PGA_scaffold9__45_contigs__length_38581958 38581958 45012577 1.1666742522502358 13.852141411224293 PGA_scaffold10__49_contigs__length_53961475 53961475 50014896 0.9268630258902301 4.724916096713111 PGA_scaffold11__79_contigs__length_51449921 51449921 45015247 0.8749332579150122 4.882377727179956 PGA_scaffold12__71_contigs__length_50438331 50438331 53047475 1.0517293881115932 6.156591479788271 PGA_scaffold13__52_contigs__length_44396874 44396874 43700117 0.9843061698443003 5.013312018665663 PGA_scaffold14__91_contigs__length_45393038 45393038 59044733 1.3007442462872831 22.9320536849055 PGA_scaffold15__101_contigs__length_47938513 47938513 39807183 0.830380011995783 3.9465800264574087 PGA_scaffold16__33_contigs__length_31980953 31980953 36208232 1.132181145446166 16.97958916124877 PGA_scaffold17__51_contigs__length_34923512 34923512 35978612 1.030211738155086 5.74339351235195 PGA_scaffold18__69_contigs__length_27737463 27737463 26601562 0.9590481292395054 7.760588019931985