view test-data/smudgeplot_verbose_summary.txt @ 3:3dd6be0cd8dd draft default tip

planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c

1n coverage estimates (Coverage of every haplotype; Don't confuse with genome coverage which is (ploidy * 1n coverage).)
* User defined 1n coverage:	
* Subset 1n coverage estimate:	41.7
* Highest peak 1n coverage estimate:	35.2
1n coverage used in smudgeplot (one of the three above):	41.7
* Proposed ploidy:	2
* Minimal number of heterozygous loci:	23132
Note: This number is NOT an estimate of the total number heterozygous loci, it's merly setting the lower boundary if the inference of heterozygosity peaks is correct.
* Proportion of heterozygosity carried by pairs in different genome copies (table)
  genome_copies propotion_of_heterozygosity
1             2                        0.53
2             3                        0.00
3             4                        0.22
4             5                        0.11
5             6                        0.14
* Proportion of heterozygosity carried by paralogs:	0.473
* Summary of all detected peaks (table)
    peak kmers [#] kmers [proportion] summit B / (A + B) summit A + B
1     AB    255991               0.53               0.49        98.62
3   AAAB    107728               0.22               0.33       160.51
5 AAAAAB     68379               0.14               0.19       253.34
4  AAAAB     53663               0.11               0.25       206.92