BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-221_S33_L004_dedup.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-221_S33_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 = 11,167,572 number of mapped reads = 11,167,572 (100%) number of mapped paired reads (first in pair) = 5,583,786 number of mapped paired reads (second in pair) = 5,583,786 number of mapped paired reads (both in pair) = 11,167,572 number of mapped paired reads (singletons) = 0 number of mapped bases = 993,996,385 bp number of sequenced bases = 988,628,774 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,355,388 duplication rate = 25.3% >>>>>>> Insert size mean insert size = 166.1292 std insert size = 98.2137 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 19.5521 >>>>>>> ACTG content number of A's = 375,667,228 bp (38%) number of C's = 120,070,228 bp (12.15%) number of T's = 374,262,174 bp (37.86%) number of G's = 118,629,144 bp (12%) number of N's = 63,759 bp (0.01%) GC percentage = 24.14% >>>>>>> Mismatches and indels general error rate = 0.2136 number of mismatches = 198,097,398 number of insertions = 4,175,258 mapped reads with insertion percentage = 22.02% number of deletions = 2,564,341 mapped reads with deletion percentage = 17.5% homopolymer indels = 39.55% >>>>>>> Coverage mean coverageData = 1.0548X std coverageData = 8.3755X There is a 31.43% of reference with a coverageData >= 1X There is a 19.27% of reference with a coverageData >= 2X There is a 11.33% of reference with a coverageData >= 3X There is a 7.78% of reference with a coverageData >= 4X There is a 5.27% of reference with a coverageData >= 5X There is a 3.88% of reference with a coverageData >= 6X There is a 2.86% of reference with a coverageData >= 7X There is a 2.22% of reference with a coverageData >= 8X There is a 1.74% of reference with a coverageData >= 9X There is a 1.42% of reference with a coverageData >= 10X There is a 1.17% of reference with a coverageData >= 11X There is a 0.99% of reference with a coverageData >= 12X There is a 0.84% of reference with a coverageData >= 13X There is a 0.73% of reference with a coverageData >= 14X There is a 0.64% of reference with a coverageData >= 15X There is a 0.57% of reference with a coverageData >= 16X There is a 0.51% of reference with a coverageData >= 17X There is a 0.46% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.35% 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 0.26% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% 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 0.19% 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 0.15% 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 0.12% 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 0.1% 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 0.09% 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 96544125 1.0769742426410769 4.088091023616385 PGA_scaffold2__36_contigs__length_69596280 69596280 76894399 1.104863636389761 5.421763626831303 PGA_scaffold3__111_contigs__length_57743597 57743597 62114573 1.0756962888889654 4.339911390032463 PGA_scaffold4__129_contigs__length_65288255 65288255 68029624 1.0419887007241961 9.861555053597197 PGA_scaffold5__109_contigs__length_67248332 67248332 63355511 0.9421127500976529 5.291211853629868 PGA_scaffold6__104_contigs__length_61759565 61759565 61598874 0.9973981196272999 6.651906307265506 PGA_scaffold7__69_contigs__length_43120122 43120122 44253683 1.0262884460299069 3.9277022462800923 PGA_scaffold8__63_contigs__length_61151155 61151155 63914461 1.0451881244107326 4.42631689102759 PGA_scaffold9__45_contigs__length_38581958 38581958 46719419 1.2109136348134535 13.709086803175905 PGA_scaffold10__49_contigs__length_53961475 53961475 52763677 0.9778027194401191 4.6432576783473145 PGA_scaffold11__79_contigs__length_51449921 51449921 47417071 0.9216160118107859 4.852031879428195 PGA_scaffold12__71_contigs__length_50438331 50438331 55825534 1.1068077173291082 6.140735875603672 PGA_scaffold13__52_contigs__length_44396874 44396874 46284855 1.0425250885906967 5.257722801254552 PGA_scaffold14__91_contigs__length_45393038 45393038 62133432 1.368787698236897 22.711517519215754 PGA_scaffold15__101_contigs__length_47938513 47938513 42323323 0.8828668298493113 3.9098206416618653 PGA_scaffold16__33_contigs__length_31980953 31980953 37966267 1.1871524591527964 16.69955402476304 PGA_scaffold17__51_contigs__length_34923512 34923512 38141711 1.0921499246696609 5.556410563762757 PGA_scaffold18__69_contigs__length_27737463 27737463 27715846 0.999220656914441 7.911616864214825