BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-188_S21_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 = 12,385,666 number of mapped reads = 12,385,666 (100%) number of mapped paired reads (first in pair) = 6,192,833 number of mapped paired reads (second in pair) = 6,192,833 number of mapped paired reads (both in pair) = 12,385,666 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,029,922,481 bp number of sequenced bases = 1,027,675,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,518,940 duplication rate = 37% >>>>>>> Insert size mean insert size = 130.1851 std insert size = 87.3319 median insert size = 106 >>>>>>> Mapping quality mean mapping quality = 24.4004 >>>>>>> ACTG content number of A's = 395,378,404 bp (38.47%) number of C's = 119,569,487 bp (11.63%) number of T's = 394,219,171 bp (38.36%) number of G's = 118,508,761 bp (11.53%) number of N's = 85,964 bp (0.01%) GC percentage = 23.17% >>>>>>> Mismatches and indels general error rate = 0.1865 number of mismatches = 187,997,811 number of insertions = 1,256,965 mapped reads with insertion percentage = 8.9% number of deletions = 1,185,481 mapped reads with deletion percentage = 8.69% homopolymer indels = 49.69% >>>>>>> Coverage mean coverageData = 1.0929X std coverageData = 7.0497X There is a 32.44% of reference with a coverageData >= 1X There is a 21.43% of reference with a coverageData >= 2X There is a 12.86% of reference with a coverageData >= 3X There is a 9.19% of reference with a coverageData >= 4X There is a 6.19% of reference with a coverageData >= 5X There is a 4.59% of reference with a coverageData >= 6X There is a 3.27% of reference with a coverageData >= 7X There is a 2.5% of reference with a coverageData >= 8X There is a 1.87% of reference with a coverageData >= 9X There is a 1.47% of reference with a coverageData >= 10X There is a 1.15% of reference with a coverageData >= 11X There is a 0.94% of reference with a coverageData >= 12X There is a 0.76% of reference with a coverageData >= 13X There is a 0.64% of reference with a coverageData >= 14X There is a 0.54% of reference with a coverageData >= 15X There is a 0.47% of reference with a coverageData >= 16X There is a 0.41% of reference with a coverageData >= 17X There is a 0.36% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 104243013 1.1628572942817488 3.8956549134347838 PGA_scaffold2__36_contigs__length_69596280 69596280 82564157 1.1863300308579712 5.342046941632917 PGA_scaffold3__111_contigs__length_57743597 57743597 65696196 1.1377226119114126 3.6593397916576955 PGA_scaffold4__129_contigs__length_65288255 65288255 71244067 1.0912233295253488 5.638685287576996 PGA_scaffold5__109_contigs__length_67248332 67248332 64231405 0.9551375192473175 3.973709837653818 PGA_scaffold6__104_contigs__length_61759565 61759565 64103338 1.037949959654023 7.138199367963558 PGA_scaffold7__69_contigs__length_43120122 43120122 45996307 1.06670168975867 3.4605769496436416 PGA_scaffold8__63_contigs__length_61151155 61151155 67015097 1.0958925796250292 3.991185431323579 PGA_scaffold9__45_contigs__length_38581958 38581958 46920811 1.2161334839460454 10.277436059925199 PGA_scaffold10__49_contigs__length_53961475 53961475 54672630 1.0131789392339627 3.1107011907431352 PGA_scaffold11__79_contigs__length_51449921 51449921 48524375 0.9431379884917608 3.9409516618471425 PGA_scaffold12__71_contigs__length_50438331 50438331 58008705 1.150091683247806 4.838790896619947 PGA_scaffold13__52_contigs__length_44396874 44396874 47602343 1.072200331041325 4.162150025838758 PGA_scaffold14__91_contigs__length_45393038 45393038 63070384 1.3894285727251832 20.331257637717314 PGA_scaffold15__101_contigs__length_47938513 47938513 42819577 0.8932187153990363 3.4677047410429966 PGA_scaffold16__33_contigs__length_31980953 31980953 37803357 1.1820584896266224 14.323202928612892 PGA_scaffold17__51_contigs__length_34923512 34923512 38391893 1.099313637185172 4.290455256268287 PGA_scaffold18__69_contigs__length_27737463 27737463 27014826 0.9739472568201353 6.114422395381449