Mercurial > repos > bgruening > erga_ear

annotate test-data/smudgeplot_verbose_summary.txt @ 1:82450f7907ef draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176
author bgruening
date Fri, 30 Aug 2024 09:27:17 +0000
parents 6af76d4371f8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
1 1n coverage estimates (Coverage of every haplotype; Don't confuse with genome coverage which is (ploidy * 1n coverage).)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
2 * User defined 1n coverage:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
3 * Subset 1n coverage estimate: 41.7
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
4 * Highest peak 1n coverage estimate: 35.2
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
5 1n coverage used in smudgeplot (one of the three above): 41.7
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
6 * Proposed ploidy: 2
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
7 * Minimal number of heterozygous loci: 23132
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
8 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.
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
9 * Proportion of heterozygosity carried by pairs in different genome copies (table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
10 genome_copies propotion_of_heterozygosity
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
11 1 2 0.53
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
12 2 3 0.00
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
13 3 4 0.22
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
14 4 5 0.11
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
15 5 6 0.14
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
16 * Proportion of heterozygosity carried by paralogs: 0.473
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
17 * Summary of all detected peaks (table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
18 peak kmers [#] kmers [proportion] summit B / (A + B) summit A + B
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
19 1 AB 255991 0.53 0.49 98.62
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
20 3 AAAB 107728 0.22 0.33 160.51
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
21 5 AAAAAB 68379 0.14 0.19 253.34
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251
bgruening
parents:
diff changeset
22 4 AAAAB 53663 0.11 0.25 206.92