BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-214_S30_L004_dedup.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-214_S30_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 = 20,265,794 number of mapped reads = 20,265,794 (100%) number of mapped paired reads (first in pair) = 10,132,897 number of mapped paired reads (second in pair) = 10,132,897 number of mapped paired reads (both in pair) = 20,265,794 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,854,419,009 bp number of sequenced bases = 1,845,008,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,726,344 duplication rate = 26.97% >>>>>>> Insert size mean insert size = 163.6796 std insert size = 92.9413 median insert size = 134 >>>>>>> Mapping quality mean mapping quality = 20.373 >>>>>>> ACTG content number of A's = 706,864,967 bp (38.31%) number of C's = 217,642,324 bp (11.8%) number of T's = 704,629,480 bp (38.19%) number of G's = 215,871,703 bp (11.7%) number of N's = 118,292 bp (0.01%) GC percentage = 23.5% >>>>>>> Mismatches and indels general error rate = 0.2098 number of mismatches = 364,698,818 number of insertions = 6,986,308 mapped reads with insertion percentage = 20.56% number of deletions = 4,395,437 mapped reads with deletion percentage = 16.76% homopolymer indels = 41.32% >>>>>>> Coverage mean coverageData = 1.9679X std coverageData = 12.3104X There is a 43.96% of reference with a coverageData >= 1X There is a 30.52% of reference with a coverageData >= 2X There is a 21.01% of reference with a coverageData >= 3X There is a 15.66% of reference with a coverageData >= 4X There is a 11.66% of reference with a coverageData >= 5X There is a 9.04% of reference with a coverageData >= 6X There is a 7.02% of reference with a coverageData >= 7X There is a 5.61% of reference with a coverageData >= 8X There is a 4.51% of reference with a coverageData >= 9X There is a 3.71% of reference with a coverageData >= 10X There is a 3.07% of reference with a coverageData >= 11X There is a 2.59% of reference with a coverageData >= 12X There is a 2.21% of reference with a coverageData >= 13X There is a 1.91% of reference with a coverageData >= 14X There is a 1.66% of reference with a coverageData >= 15X There is a 1.46% of reference with a coverageData >= 16X There is a 1.3% of reference with a coverageData >= 17X There is a 1.16% of reference with a coverageData >= 18X There is a 1.05% of reference with a coverageData >= 19X There is a 0.95% of reference with a coverageData >= 20X There is a 0.87% of reference with a coverageData >= 21X There is a 0.8% of reference with a coverageData >= 22X There is a 0.74% of reference with a coverageData >= 23X There is a 0.68% of reference with a coverageData >= 24X There is a 0.63% of reference with a coverageData >= 25X There is a 0.59% of reference with a coverageData >= 26X There is a 0.55% of reference with a coverageData >= 27X There is a 0.52% of reference with a coverageData >= 28X There is a 0.49% of reference with a coverageData >= 29X There is a 0.46% of reference with a coverageData >= 30X There is a 0.44% of reference with a coverageData >= 31X There is a 0.41% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.37% of reference with a coverageData >= 34X There is a 0.36% of reference with a coverageData >= 35X There is a 0.34% of reference with a coverageData >= 36X There is a 0.32% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.3% of reference with a coverageData >= 39X There is a 0.28% of reference with a coverageData >= 40X There is a 0.27% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.25% of reference with a coverageData >= 43X There is a 0.24% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.23% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 182203632 2.0325278061161516 6.55682932631896 PGA_scaffold2__36_contigs__length_69596280 69596280 145591381 2.091941997474578 8.968478151427464 PGA_scaffold3__111_contigs__length_57743597 57743597 116373590 2.015350550468825 7.052718134437175 PGA_scaffold4__129_contigs__length_65288255 65288255 127624568 1.9547860177914083 14.975077755164973 PGA_scaffold5__109_contigs__length_67248332 67248332 118566986 1.7631215893949608 8.624682573845577 PGA_scaffold6__104_contigs__length_61759565 61759565 115084490 1.8634277945448612 9.69455580700066 PGA_scaffold7__69_contigs__length_43120122 43120122 82297733 1.9085691130465725 6.432919732340764 PGA_scaffold8__63_contigs__length_61151155 61151155 119594411 1.9557179418769768 7.064404332392896 PGA_scaffold9__45_contigs__length_38581958 38581958 86253260 2.2355853479494225 21.784327128438797 PGA_scaffold10__49_contigs__length_53961475 53961475 98520656 1.8257591364950643 6.575307085420553 PGA_scaffold11__79_contigs__length_51449921 51449921 89589318 1.74129165329525 7.752268355554089 PGA_scaffold12__71_contigs__length_50438331 50438331 103945633 2.060846006185256 9.187754071284768 PGA_scaffold13__52_contigs__length_44396874 44396874 85974094 1.9364898078184514 8.544561246909081 PGA_scaffold14__91_contigs__length_45393038 45393038 113334050 2.496727581881609 30.113432762639906 PGA_scaffold15__101_contigs__length_47938513 47938513 78895161 1.6457573684023115 6.447044080712683 PGA_scaffold16__33_contigs__length_31980953 31980953 69567532 2.175280142527335 24.306648238621918 PGA_scaffold17__51_contigs__length_34923512 34923512 69876705 2.000849885887765 7.808035681726728 PGA_scaffold18__69_contigs__length_27737463 27737463 51125809 1.8432042252746763 13.0972274548548