BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-214_S30_L004_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 = 17,407,756 number of mapped reads = 17,407,756 (100%) number of mapped paired reads (first in pair) = 8,703,878 number of mapped paired reads (second in pair) = 8,703,878 number of mapped paired reads (both in pair) = 17,407,756 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,537,917,193 bp number of sequenced bases = 1,534,514,507 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,140,300 duplication rate = 32.06% >>>>>>> Insert size mean insert size = 146.9177 std insert size = 90.2035 median insert size = 123 >>>>>>> Mapping quality mean mapping quality = 24.5176 >>>>>>> ACTG content number of A's = 591,495,789 bp (38.55%) number of C's = 177,076,827 bp (11.54%) number of T's = 590,023,407 bp (38.45%) number of G's = 175,918,484 bp (11.46%) number of N's = 91,964 bp (0.01%) GC percentage = 23% >>>>>>> Mismatches and indels general error rate = 0.1866 number of mismatches = 280,868,503 number of insertions = 1,851,369 mapped reads with insertion percentage = 9.29% number of deletions = 1,788,851 mapped reads with deletion percentage = 9.29% homopolymer indels = 50.25% >>>>>>> Coverage mean coverageData = 1.632X std coverageData = 8.9033X There is a 40.58% of reference with a coverageData >= 1X There is a 27.92% of reference with a coverageData >= 2X There is a 18.79% of reference with a coverageData >= 3X There is a 13.91% of reference with a coverageData >= 4X There is a 10.17% of reference with a coverageData >= 5X There is a 7.8% of reference with a coverageData >= 6X There is a 5.93% of reference with a coverageData >= 7X There is a 4.66% of reference with a coverageData >= 8X There is a 3.65% of reference with a coverageData >= 9X There is a 2.93% of reference with a coverageData >= 10X There is a 2.36% of reference with a coverageData >= 11X There is a 1.94% of reference with a coverageData >= 12X There is a 1.61% of reference with a coverageData >= 13X There is a 1.36% of reference with a coverageData >= 14X There is a 1.15% of reference with a coverageData >= 15X There is a 0.99% of reference with a coverageData >= 16X There is a 0.86% of reference with a coverageData >= 17X There is a 0.75% of reference with a coverageData >= 18X There is a 0.67% of reference with a coverageData >= 19X There is a 0.6% of reference with a coverageData >= 20X There is a 0.54% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.44% of reference with a coverageData >= 23X There is a 0.41% of reference with a coverageData >= 24X There is a 0.38% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 156416098 1.7448613126942987 5.113731793321025 PGA_scaffold2__36_contigs__length_69596280 69596280 124192753 1.7844740121167395 7.255018107408274 PGA_scaffold3__111_contigs__length_57743597 57743597 97875416 1.6950003305128358 5.316769190719557 PGA_scaffold4__129_contigs__length_65288255 65288255 105223238 1.6116717777186724 7.749171958554545 PGA_scaffold5__109_contigs__length_67248332 67248332 96221590 1.4308398013500172 5.53509684253319 PGA_scaffold6__104_contigs__length_61759565 61759565 94632337 1.5322701349985222 7.823017738795794 PGA_scaffold7__69_contigs__length_43120122 43120122 68331955 1.5846883503715505 4.887200434061181 PGA_scaffold8__63_contigs__length_61151155 61151155 100424476 1.6422335113703086 5.6179727731272235 PGA_scaffold9__45_contigs__length_38581958 38581958 69639774 1.8049828886341124 14.374077458649536 PGA_scaffold10__49_contigs__length_53961475 53961475 82497740 1.5288266304803566 4.434028652697994 PGA_scaffold11__79_contigs__length_51449921 51449921 74008504 1.4384570969506445 6.083658261517226 PGA_scaffold12__71_contigs__length_50438331 50438331 87500135 1.7347944165717935 6.538160511050628 PGA_scaffold13__52_contigs__length_44396874 44396874 71303270 1.606042578583348 6.006066935633644 PGA_scaffold14__91_contigs__length_45393038 45393038 93341868 2.0563036120208564 24.521629316825656 PGA_scaffold15__101_contigs__length_47938513 47938513 63894653 1.3328459520636362 4.916309020758231 PGA_scaffold16__33_contigs__length_31980953 31980953 55344215 1.730536766681093 15.753264915068241 PGA_scaffold17__51_contigs__length_34923512 34923512 56873873 1.62852673579908 5.376218582147923 PGA_scaffold18__69_contigs__length_27737463 27737463 40195298 1.449133902404845 8.946244251355012