BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-176_S15_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 = 20,189,372 number of mapped reads = 20,189,372 (100%) number of mapped paired reads (first in pair) = 10,094,686 number of mapped paired reads (second in pair) = 10,094,686 number of mapped paired reads (both in pair) = 20,189,372 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,820,216,229 bp number of sequenced bases = 1,816,075,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,955,466 duplication rate = 30.13% >>>>>>> Insert size mean insert size = 149.15 std insert size = 86.8056 median insert size = 126 >>>>>>> Mapping quality mean mapping quality = 24.5799 >>>>>>> ACTG content number of A's = 705,692,335 bp (38.86%) number of C's = 203,632,414 bp (11.21%) number of T's = 704,156,324 bp (38.77%) number of G's = 202,594,465 bp (11.16%) number of N's = 164,004 bp (0.01%) GC percentage = 22.37% >>>>>>> Mismatches and indels general error rate = 0.1852 number of mismatches = 329,903,862 number of insertions = 2,215,730 mapped reads with insertion percentage = 9.57% number of deletions = 2,157,188 mapped reads with deletion percentage = 9.66% homopolymer indels = 50.9% >>>>>>> Coverage mean coverageData = 1.9316X std coverageData = 10.5072X There is a 45.02% of reference with a coverageData >= 1X There is a 31.99% of reference with a coverageData >= 2X There is a 22.29% of reference with a coverageData >= 3X There is a 16.78% of reference with a coverageData >= 4X There is a 12.53% of reference with a coverageData >= 5X There is a 9.72% of reference with a coverageData >= 6X There is a 7.5% of reference with a coverageData >= 7X There is a 5.94% of reference with a coverageData >= 8X There is a 4.69% of reference with a coverageData >= 9X There is a 3.78% of reference with a coverageData >= 10X There is a 3.05% of reference with a coverageData >= 11X There is a 2.51% of reference with a coverageData >= 12X There is a 2.07% of reference with a coverageData >= 13X There is a 1.74% of reference with a coverageData >= 14X There is a 1.47% of reference with a coverageData >= 15X There is a 1.26% of reference with a coverageData >= 16X There is a 1.08% of reference with a coverageData >= 17X There is a 0.95% of reference with a coverageData >= 18X There is a 0.83% of reference with a coverageData >= 19X There is a 0.74% of reference with a coverageData >= 20X There is a 0.66% of reference with a coverageData >= 21X There is a 0.6% of reference with a coverageData >= 22X There is a 0.54% of reference with a coverageData >= 23X There is a 0.5% of reference with a coverageData >= 24X There is a 0.45% of reference with a coverageData >= 25X There is a 0.42% of reference with a coverageData >= 26X There is a 0.39% of reference with a coverageData >= 27X There is a 0.36% of reference with a coverageData >= 28X There is a 0.34% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.27% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% 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 185045137 2.064225516311731 6.225105773086893 PGA_scaffold2__36_contigs__length_69596280 69596280 147480255 2.1190824423374353 8.66333738527532 PGA_scaffold3__111_contigs__length_57743597 57743597 115852417 2.0063249090630775 5.786169876059984 PGA_scaffold4__129_contigs__length_65288255 65288255 125484963 1.9220143500542326 8.558838245644088 PGA_scaffold5__109_contigs__length_67248332 67248332 112966438 1.6798399996002875 5.912305045579992 PGA_scaffold6__104_contigs__length_61759565 61759565 112311859 1.8185338416810417 11.06097017471459 PGA_scaffold7__69_contigs__length_43120122 43120122 82353397 1.9098600184851053 5.409055753171633 PGA_scaffold8__63_contigs__length_61151155 61151155 118102571 1.931322000377589 5.814560509730063 PGA_scaffold9__45_contigs__length_38581958 38581958 82192108 2.1303249565509352 15.681752333114378 PGA_scaffold10__49_contigs__length_53961475 53961475 97372478 1.8044814008512555 4.816624292364999 PGA_scaffold11__79_contigs__length_51449921 51449921 87654045 1.7036769599704535 6.398509652799908 PGA_scaffold12__71_contigs__length_50438331 50438331 103367082 2.049375543373947 7.61996916026023 PGA_scaffold13__52_contigs__length_44396874 44396874 84428035 1.9016662074000976 6.547304787488322 PGA_scaffold14__91_contigs__length_45393038 45393038 108486738 2.389942219773878 26.908485127058274 PGA_scaffold15__101_contigs__length_47938513 47938513 76495716 1.5957048146236827 5.362212106320555 PGA_scaffold16__33_contigs__length_31980953 31980953 66621405 2.0831588414516604 24.45723775385127 PGA_scaffold17__51_contigs__length_34923512 34923512 67352216 1.928563656484491 6.864992961595007 PGA_scaffold18__69_contigs__length_27737463 27737463 46649369 1.681818160514536 9.787226122519977