BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-184_S18_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 = 12,592,924 number of mapped reads = 12,592,924 (100%) number of mapped paired reads (first in pair) = 6,296,462 number of mapped paired reads (second in pair) = 6,296,462 number of mapped paired reads (both in pair) = 12,592,924 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,102,113,789 bp number of sequenced bases = 1,099,636,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,291,484 duplication rate = 32.11% >>>>>>> Insert size mean insert size = 142.5219 std insert size = 88.853 median insert size = 118 >>>>>>> Mapping quality mean mapping quality = 23.9969 >>>>>>> ACTG content number of A's = 422,686,640 bp (38.44%) number of C's = 128,471,680 bp (11.68%) number of T's = 421,397,270 bp (38.32%) number of G's = 127,080,636 bp (11.56%) number of N's = 96,215 bp (0.01%) GC percentage = 23.24% >>>>>>> Mismatches and indels general error rate = 0.1878 number of mismatches = 202,417,938 number of insertions = 1,377,822 mapped reads with insertion percentage = 9.57% number of deletions = 1,299,833 mapped reads with deletion percentage = 9.34% homopolymer indels = 49.5% >>>>>>> Coverage mean coverageData = 1.1695X std coverageData = 8.2159X There is a 33.85% of reference with a coverageData >= 1X There is a 22.06% of reference with a coverageData >= 2X There is a 13.55% of reference with a coverageData >= 3X There is a 9.62% of reference with a coverageData >= 4X There is a 6.6% of reference with a coverageData >= 5X There is a 4.88% of reference with a coverageData >= 6X There is a 3.55% of reference with a coverageData >= 7X There is a 2.72% of reference with a coverageData >= 8X There is a 2.07% of reference with a coverageData >= 9X There is a 1.64% of reference with a coverageData >= 10X There is a 1.3% of reference with a coverageData >= 11X There is a 1.07% of reference with a coverageData >= 12X There is a 0.88% of reference with a coverageData >= 13X There is a 0.75% of reference with a coverageData >= 14X There is a 0.64% of reference with a coverageData >= 15X There is a 0.55% of reference with a coverageData >= 16X There is a 0.48% of reference with a coverageData >= 17X There is a 0.43% of reference with a coverageData >= 18X There is a 0.38% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.32% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 112858190 1.2589617825123254 3.924930507542253 PGA_scaffold2__36_contigs__length_69596280 69596280 89877922 1.29141847811406 6.419391084078098 PGA_scaffold3__111_contigs__length_57743597 57743597 69276084 1.1997188883124132 4.032669309942571 PGA_scaffold4__129_contigs__length_65288255 65288255 74106427 1.1350652119588738 6.557867914391484 PGA_scaffold5__109_contigs__length_67248332 67248332 68506616 1.018711006839545 4.476626909086883 PGA_scaffold6__104_contigs__length_61759565 61759565 66878621 1.0828868532347986 6.2994443369307005 PGA_scaffold7__69_contigs__length_43120122 43120122 48635759 1.1279132976479056 3.9941315381311235 PGA_scaffold8__63_contigs__length_61151155 61151155 71203318 1.1643822263046382 4.189656034584663 PGA_scaffold9__45_contigs__length_38581958 38581958 50486698 1.3085571758696124 12.167753508729792 PGA_scaffold10__49_contigs__length_53961475 53961475 60410768 1.1195166181057874 3.5749815808579464 PGA_scaffold11__79_contigs__length_51449921 51449921 51609926 1.003109917311632 4.948634924007545 PGA_scaffold12__71_contigs__length_50438331 50438331 63397854 1.2569379823452127 5.492838643528403 PGA_scaffold13__52_contigs__length_44396874 44396874 51252482 1.1544164573388658 4.656678022469158 PGA_scaffold14__91_contigs__length_45393038 45393038 69108851 1.5224548530988387 26.138698724139974 PGA_scaffold15__101_contigs__length_47938513 47938513 44801728 0.9345664935414246 3.77460325915505 PGA_scaffold16__33_contigs__length_31980953 31980953 40392134 1.263005952324185 13.71402483767366 PGA_scaffold17__51_contigs__length_34923512 34923512 40340135 1.1550996073934374 4.2487341633676445 PGA_scaffold18__69_contigs__length_27737463 27737463 28970276 1.0444457735734518 7.4754541776395325