BamQC report
-----------------------------------
>>>>>>> Input
bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-206_S27_L004_dedup.sorted.bam
outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-206_S27_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 = 14,990,294
number of mapped reads = 14,990,294 (100%)
number of mapped paired reads (first in pair) = 7,495,147
number of mapped paired reads (second in pair) = 7,495,147
number of mapped paired reads (both in pair) = 14,990,294
number of mapped paired reads (singletons) = 0
number of mapped bases = 1,329,405,753 bp
number of sequenced bases = 1,322,532,951 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 4,998,789
duplication rate = 27.53%
>>>>>>> Insert size
mean insert size = 160.6348
std insert size = 94.8136
median insert size = 129
>>>>>>> Mapping quality
mean mapping quality = 19.7052
>>>>>>> ACTG content
number of A's = 502,073,672 bp (37.96%)
number of C's = 161,337,485 bp (12.2%)
number of T's = 499,971,965 bp (37.8%)
number of G's = 159,149,829 bp (12.03%)
number of N's = 84,176 bp (0.01%)
GC percentage = 24.23%
>>>>>>> Mismatches and indels
general error rate = 0.2113
number of mismatches = 262,632,201
number of insertions = 5,255,067
mapped reads with insertion percentage = 21%
number of deletions = 3,246,933
mapped reads with deletion percentage = 16.71%
homopolymer indels = 40.07%
>>>>>>> Coverage
mean coverageData = 1.4107X
std coverageData = 11.1269X
There is a 35.76% of reference with a coverageData >= 1X
There is a 23.41% of reference with a coverageData >= 2X
There is a 14.82% of reference with a coverageData >= 3X
There is a 10.69% of reference with a coverageData >= 4X
There is a 7.62% of reference with a coverageData >= 5X
There is a 5.8% of reference with a coverageData >= 6X
There is a 4.41% of reference with a coverageData >= 7X
There is a 3.5% of reference with a coverageData >= 8X
There is a 2.79% of reference with a coverageData >= 9X
There is a 2.3% of reference with a coverageData >= 10X
There is a 1.9% of reference with a coverageData >= 11X
There is a 1.61% of reference with a coverageData >= 12X
There is a 1.38% of reference with a coverageData >= 13X
There is a 1.2% of reference with a coverageData >= 14X
There is a 1.05% of reference with a coverageData >= 15X
There is a 0.93% of reference with a coverageData >= 16X
There is a 0.83% of reference with a coverageData >= 17X
There is a 0.75% of reference with a coverageData >= 18X
There is a 0.68% of reference with a coverageData >= 19X
There is a 0.62% of reference with a coverageData >= 20X
There is a 0.57% of reference with a coverageData >= 21X
There is a 0.53% of reference with a coverageData >= 22X
There is a 0.49% of reference with a coverageData >= 23X
There is a 0.45% of reference with a coverageData >= 24X
There is a 0.42% of reference with a coverageData >= 25X
There is a 0.4% of reference with a coverageData >= 26X
There is a 0.37% of reference with a coverageData >= 27X
There is a 0.35% of reference with a coverageData >= 28X
There is a 0.33% of reference with a coverageData >= 29X
There is a 0.31% 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 0.2% of reference with a coverageData >= 40X
There is a 0.19% of reference with a coverageData >= 41X
There is a 0.18% of reference with a coverageData >= 42X
There is a 0.17% of reference with a coverageData >= 43X
There is a 0.17% of reference with a coverageData >= 44X
There is a 0.16% of reference with a coverageData >= 45X
There is a 0.16% of reference with a coverageData >= 46X
There is a 0.15% of reference with a coverageData >= 47X
There is a 0.15% of reference with a coverageData >= 48X
There is a 0.14% of reference with a coverageData >= 49X
There is a 0.14% of reference with a coverageData >= 50X
There is a 0.13% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
PGA_scaffold1__77_contigs__length_89643857 89643857 130649928 1.4574331401202427 6.000186331456102
PGA_scaffold2__36_contigs__length_69596280 69596280 104227843 1.497606524371705 7.565950686525204
PGA_scaffold3__111_contigs__length_57743597 57743597 82616076 1.4307400351245871 5.4391124031375835
PGA_scaffold4__129_contigs__length_65288255 65288255 90371380 1.3841904642726321 11.824728141534573
PGA_scaffold5__109_contigs__length_67248332 67248332 85093262 1.2653587006440545 6.988775161273332
PGA_scaffold6__104_contigs__length_61759565 61759565 82144727 1.3300729530721274 9.913630285252092
PGA_scaffold7__69_contigs__length_43120122 43120122 58457371 1.3556865864155023 5.2681267955415
PGA_scaffold8__63_contigs__length_61151155 61151155 85285701 1.3946703214354659 5.609714938516048
PGA_scaffold9__45_contigs__length_38581958 38581958 62235356 1.6130688857211446 17.416155693067548
PGA_scaffold10__49_contigs__length_53961475 53961475 71545786 1.3258678714768268 5.710494210004391
PGA_scaffold11__79_contigs__length_51449921 51449921 62274416 1.2103889527838148 6.589331096537315
PGA_scaffold12__71_contigs__length_50438331 50438331 74982490 1.486617191992336 7.730945350718315
PGA_scaffold13__52_contigs__length_44396874 44396874 62143497 1.399726859147786 7.223030579148235
PGA_scaffold14__91_contigs__length_45393038 45393038 83489939 1.8392674885518787 28.548166862026864
PGA_scaffold15__101_contigs__length_47938513 47938513 55976578 1.1676744750092687 5.458661448805083
PGA_scaffold16__33_contigs__length_31980953 31980953 50508862 1.579341991465983 25.925566897404426
PGA_scaffold17__51_contigs__length_34923512 34923512 50481645 1.4454916504388218 7.34975201434325
PGA_scaffold18__69_contigs__length_27737463 27737463 36920896 1.3310841009504006 10.90024750447339