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

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planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c
author bgruening
date Tue, 15 Oct 2024 12:52:59 +0000
parents 8c99976de71e
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8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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1 1n coverage estimates (Coverage of every haplotype; Don't confuse with genome coverage which is (ploidy * 1n coverage).)
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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2 * User defined 1n coverage:
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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3 * Subset 1n coverage estimate: 41.7
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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4 * Highest peak 1n coverage estimate: 35.2
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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5 1n coverage used in smudgeplot (one of the three above): 41.7
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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6 * Proposed ploidy: 2
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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7 * Minimal number of heterozygous loci: 23132
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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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.
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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9 * Proportion of heterozygosity carried by pairs in different genome copies (table)
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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10 genome_copies propotion_of_heterozygosity
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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11 1 2 0.53
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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12 2 3 0.00
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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13 3 4 0.22
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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14 4 5 0.11
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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15 5 6 0.14
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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16 * Proportion of heterozygosity carried by paralogs: 0.473
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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17 * Summary of all detected peaks (table)
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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18 peak kmers [#] kmers [proportion] summit B / (A + B) summit A + B
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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19 1 AB 255991 0.53 0.49 98.62
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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20 3 AAAB 107728 0.22 0.33 160.51
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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21 5 AAAAAB 68379 0.14 0.19 253.34
8c99976de71e planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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22 4 AAAAB 53663 0.11 0.25 206.92