Raccoon mask report
Masking file application report, summarizing the number and percentage of masked sites, and any sequences removed due to masking.
Masking file application report, summarizing the number and percentage of masked sites, and any sequences removed due to masking.
Sequences: 51
Alignment length: 3244
Masked sites: 11
Masked fraction: 0.0034
Sequences removed: 0
Mask character: ?
| flagged | type | Minimum | Maximum | Length | present_in | note |
|---|---|---|---|---|---|---|
| 25 | site | 25 | 25 | 1 | PHL036|mylona_marsh|elliville|2026-02-19 | N_adjacent |
| 46 | site | 46 | 46 | 1 | LHFV004|wilkins_sound|samford|1982 | gap_adjacent |
| 189 | site | 189 | 189 | 1 | LHFV010|mylona_marsh|elliville|1990 | N_adjacent |
| 574 | site | 574 | 574 | 1 | LHFV010|mylona_marsh|elliville|1990 | N_adjacent |
| 678 | site | 678 | 678 | 1 | LHFV010|mylona_marsh|elliville|1990 | N_adjacent |
| 1160 | site | 1160 | 1160 | 1 | LHFV001|mylona_marsh|elliville|2010 | N_adjacent |
| 2436 | site | 2436 | 2436 | 1 | LHFV007|outer_otooles|inis_aine|2005 | N_adjacent;clustered_snps |
| 2437 | site | 2437 | 2437 | 1 | LHFV007|outer_otooles|inis_aine|2005 | N_adjacent;clustered_snps |
| 2439 | site | 2439 | 2439 | 1 | LHFV007|outer_otooles|inis_aine|2005 | clustered_snps |
| 2440 | site | 2440 | 2440 | 1 | LHFV007|outer_otooles|inis_aine|2005 | clustered_snps |
| 2441 | site | 2441 | 2441 | 1 | LHFV007|outer_otooles|inis_aine|2005 | clustered_snps |
Red blocks represent masked positions along the alignment for each sequence. This plot may be downsampled for performance: every 1 sequence(s) and 2-bp windows are shown.
| sequence | masked_sites | masked_pct |
|---|---|---|
| PHL043|mylona_marsh|duggan_demesne|2026-02-28 | 11 | 0.0034 |
| PHL036|mylona_marsh|elliville|2026-02-19 | 11 | 0.0034 |
| PHL029|mylona_marsh|myra_myre|2026-02-14 | 11 | 0.0034 |
| PHL042|mylona_marsh|myra_myre|2026-02-27 | 11 | 0.0034 |
| PHL039|mylona_marsh|myra_myre|2026-02-24 | 11 | 0.0034 |
| PHL009|mylona_marsh|morang_a_moor|2026-01-20 | 11 | 0.0034 |
| PHL034|mylona_marsh|joyce_jungle|2026-02-18 | 11 | 0.0034 |
| PHL037|mylona_marsh|joyce_jungle|2026-02-20 | 11 | 0.0034 |
| PHL027|mylona_marsh|myra_myre|2026-02-11 | 11 | 0.0034 |
| PHL024|mylona_marsh|lusamaki_lake|2026-02-10 | 11 | 0.0034 |
| PHL025|mylona_marsh|elliville|2026-02-10 | 11 | 0.0034 |
| PHL031|mylona_marsh|elliville|2026-02-16 | 11 | 0.0034 |
| PHL038|mylona_marsh|elliville|2026-02-20 | 11 | 0.0034 |
| PHL035|mylona_marsh|elliville|2026-02-18 | 11 | 0.0034 |
| PHL030|mylona_marsh|elliville|2026-02-15 | 11 | 0.0034 |
| PHL033|mylona_marsh|elliville|2026-02-17 | 11 | 0.0034 |
| PHL041|mylona_marsh|lililand|2026-02-26 | 11 | 0.0034 |
| PHL001|mylona_marsh|morang_a_moor|2025-12-03 | 11 | 0.0034 |
| PHL032|lomanland|nickopolis|2026-02-16 | 11 | 0.0034 |
| PHL002|mylona_marsh|morang_a_moor|2025-12-08 | 11 | 0.0034 |
| PHL003|mylona_marsh|morang_a_moor|2025-12-28 | 11 | 0.0034 |
| PHL018|mylona_marsh|elliville|2026-02-07 | 11 | 0.0034 |
| PHL040|mylona_marsh|elliville|2026-02-24 | 11 | 0.0034 |
| PHL020|mylona_marsh|elliville|2026-02-08 | 11 | 0.0034 |
| PHL019|mylona_marsh|lililand|2026-02-07 | 11 | 0.0034 |
| PHL014|mylona_marsh|morang_a_moor|2026-02-01 | 11 | 0.0034 |
| PHL028|mylona_marsh|morang_a_moor|2026-02-11 | 11 | 0.0034 |
| PHL021|mylona_marsh|lililand|2026-02-08 | 11 | 0.0034 |
| PHL016|mylona_marsh|lililand|2026-02-05 | 11 | 0.0034 |
| PHL013|mylona_marsh|lililand|2026-01-30 | 11 | 0.0034 |
| PHL026|mylona_marsh|elliville|2026-02-10 | 11 | 0.0034 |
| PHL010|mylona_marsh|bedeburgh|2026-01-20 | 11 | 0.0034 |
| PHL007|mylona_marsh|bedeburgh|2026-01-10 | 11 | 0.0034 |
| PHL023|lomanland|nickopolis|2026-02-09 | 11 | 0.0034 |
| PHL022|lomanland|nickopolis|2026-02-08 | 11 | 0.0034 |
| PHL008|mylona_marsh|faux_kent|2026-01-17 | 11 | 0.0034 |
| PHL017|mylona_marsh|donkor_dale|2026-02-06 | 11 | 0.0034 |
| PHL004|mylona_marsh|quaye_quay|2026-01-02 | 11 | 0.0034 |
| PHL015|mylona_marsh|maloney_mere|2026-02-01 | 11 | 0.0034 |
| PHL005|mylona_marsh|donkor_dale|2026-01-03 | 11 | 0.0034 |
| PHL012|mylona_marsh|lusamaki_lake|2026-01-26 | 11 | 0.0034 |
| PHL011|mylona_marsh|elliville|2026-01-23 | 11 | 0.0034 |
| PHL006|mylona_marsh|elliville|2026-01-05 | 11 | 0.0034 |
| LHFV001|mylona_marsh|elliville|2010 | 11 | 0.0034 |
| LHFV002|lomanland|radsborough|2006 | 11 | 0.0034 |
| LHFV003|goodfellow_forest|glenian|2007 | 11 | 0.0034 |
| LHFV004|wilkins_sound|samford|1982 | 11 | 0.0034 |
| LHFV005|goodfellow_forest|glenian|1990 | 11 | 0.0034 |
| LHFV006|willmott_woods|hannahland|2019 | 11 | 0.0034 |
| LHFV007|outer_otooles|inis_aine|2005 | 11 | 0.0034 |
| LHFV010|mylona_marsh|elliville|1990 | 11 | 0.0034 |
Alignment: cases_background.aln.fasta
Mask File: mask_sites.csv
Output Alignment: cases_background.aln.masked.fasta
Outdir:
Command: raccoon mask examples/lhfv/aln-qc/cases_background.aln.fasta --mask-file examples/lhfv/aln-qc/mask_sites.csv -d examples/lhfv/masked/
Generated: 2026-03-09 16:51
Raccoon version: 1.0.0
Python: 3.14.2
Platform: Darwin 24.4.0