Raccoon seq-qc report

1. Report Summary

FASTA files: 2
Metadata files: 2

Total sequences: 53

Filters: Minimum length: 2000
Filtered: 1

Unique locations: 19

Date range: 1982 → 2026-02-28

2. Input files

FASTA files provided: cases.fasta, historical_outbreaks.fasta.

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File	Seqs	Length (min)	Length (max)	Length (mean)	N (min)	N (max)	N (mean)
cases.fasta	43	3107	3107	3107.0	0.0151	0.0267	0.0164

ID	Length	N content	Status
PHL043	3107	0.0151	kept
PHL036	3107	0.0151	kept
PHL029	3107	0.0151	kept
PHL042	3107	0.0151	kept
PHL039	3107	0.0151	kept
PHL009	3107	0.0151	kept
PHL034	3107	0.0151	kept
PHL037	3107	0.0183	kept
PHL027	3107	0.0183	kept
PHL024	3107	0.0151	kept
PHL025	3107	0.0193	kept
PHL031	3107	0.0151	kept
PHL038	3107	0.0151	kept
PHL035	3107	0.0151	kept
PHL030	3107	0.0151	kept
PHL033	3107	0.0151	kept
PHL041	3107	0.0151	kept
PHL001	3107	0.0267	kept
PHL032	3107	0.0151	kept
PHL002	3107	0.0203	kept
PHL003	3107	0.0203	kept
PHL018	3107	0.0151	kept
PHL040	3107	0.0151	kept
PHL020	3107	0.0151	kept
PHL019	3107	0.0151	kept
PHL014	3107	0.0151	kept
PHL028	3107	0.0151	kept
PHL021	3107	0.0196	kept
PHL016	3107	0.0151	kept
PHL013	3107	0.02	kept
PHL026	3107	0.0151	kept
PHL010	3107	0.0151	kept
PHL007	3107	0.0151	kept
PHL023	3107	0.0151	kept
PHL022	3107	0.0151	kept
PHL008	3107	0.0151	kept
PHL017	3107	0.0151	kept
PHL004	3107	0.0206	kept
PHL015	3107	0.0151	kept
PHL005	3107	0.0151	kept
PHL012	3107	0.0151	kept
PHL011	3107	0.0212	kept
PHL006	3107	0.0151	kept

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File	Seqs	Length (min)	Length (max)	Length (mean)	N (min)	N (max)	N (mean)
historical_outbreaks.fasta	10	132	3244	2908.9	0.0	0.8237	0.0922

ID	Length	N content	Status
LHFV001	3244	0.0003	kept
LHFV002	3210	0.0	kept
LHFV003	3244	0.0	kept
LHFV004	3196	0.0	kept
LHFV005	3225	0.0	kept
LHFV006	3213	0.0	kept
LHFV007	3200	0.0006	kept
LHFV008	132	0.0	filtered
LHFV009	3200	0.8237	kept
LHFV010	3225	0.0971	kept

Metadata files provided: case_metadata.csv, historical_outbreaks_metadata.tsv.

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Metadata file	Rows	sample	admin0	admin1	admin2	date	travel history	notes
case_metadata.csv	43

sample	admin0	admin1	admin2	date	travel history	notes
PHL001	Articia	Mylona Marsh	Morang'a Moor	2025-12-03
PHL002	Articia	Mylona Marsh	Morang'a Moor	2025-12-08
PHL003	Articia	Mylona Marsh	Morang'a Moor	2025-12-28
PHL004	Articia	Mylona Marsh	Quaye Quay	2026-01-02
PHL005	Articia	Mylona Marsh	Donkor Dale	2026-01-03
PHL006	Articia	Mylona Marsh	Elliville	2026-01-05
PHL007	Articia	Mylona Marsh	Bedeburgh	2026-01-10
PHL008	Articia	Mylona Marsh	Faux Kent	2026-01-17
PHL009	Articia	Mylona Marsh	Morang'a Moor	2026-01-20
PHL010	Articia	Mylona Marsh	Bedeburgh	2026-01-20
PHL011	Articia	Mylona Marsh	Elliville	2026-01-23
PHL012	Articia	MYLONA MARSH	Lusamaki Lake	2026-01-26
PHL013	Articia	Mylona Marsh	Lililand	2026-01-30		from SSE
PHL014	Articia	Mylona Marsh	Morang'a Moor	2026-02-01
PHL015	Articia	Mylona Marsh	Maloney Mere	2026-02-01
PHL016	Articia	Mylona Marsh	Lililand	2026-02-05
PHL017	Articia	Mylona Marsh	Donkor Dale	2026-02-06
PHL018	Articia	Mylona Marsh	Elliville	2026-02-07
PHL019	Articia	Mylona Marsh	Lililand	2026-02-07
PHL020	ARTICIA	Mylona Marsh	Elliville	2026-02-08
PHL021	ARTICIA	MYLONA MARSH	Lililand	2026-02-08
PHL022	Articia	Lomanland	Nickopolis	2026-02-08	none	Lomanland index (no travel history - missing links?)
PHL023	Articia	Lomanland	Nickopolis	2026-02-09		Lomanland outbreak
PHL024	Articia	Mylona Marsh	Lusamaki Lake	2026-02-10		super spreading event (SSE) index
PHL025	Articia	Mylona Marsh	Elliville	2026-02-10		from SSE
PHL026	Articia	Mylona Marsh	Elliville	2026-02-10		from SSE
PHL027	ARTICIA	MYLONA MARSH	Myra Myre	2026-02-11
PHL028	Articia	Mylona Marsh	Morang'a Moor	2026-02-11
PHL029	Articia	Mylona Marsh	Myra Myre	2026-02-14
PHL030	Articia	Mylona Marsh	Elliville	2026-02-15		secondary case of SSE (contact of PHL026)
PHL031	Articia	Mylona Marsh	Elliville	2026-02-16		from SSE
PHL032	Articia	Lomanland	Nickopolis	2026-02-16		Lomanland outbreak
PHL033	Articia	Mylona Marsh	Elliville	17-02-2026		from SSE
PHL034	Articia	Mylona Marsh	Joyce Jungle	18/02/2026
PHL035	Articia	Mylona Marsh	Elliville	2026-02-18		from SSE
PHL036	Articia	Mylona Marsh	Elliville	2026-02-19
PHL037	Articia	Mylona Marsh	Joyce Jungle	2026-02-20
PHL038	Articia	Mylona Marsh	Elliville	2026-02-20		from SSE
PHL039	Articia	Mylona Marsh	Myra Myre	2026-02-24
PHL040	Articia	Mylona Marsh	Elliville	2026-02-24
PHL041	Articia	Mylona Marsh	Lililand	2026-02-26		from SSE
PHL042	Articia	Mylona Marsh	Myra Myre	2026-02-27
PHL043	Articia	Mylona Marsh	Duggan Demesne	2026-02-28	Goodfellow Forest	new zoonosis (travel link to Goodfellow Forest)

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Metadata file	Rows	sample	admin1	admin2	date
historical_outbreaks_metadata.tsv	10

sample	admin1	admin2	date
LHFV001	Mylona marsh	Elliville	2010
LHFV002	Lomanland	Radsborough	2006
LHFV003	Goodfellow forest	Glenian	2007
LHFV004	Wilkins sound	Samford	1982
LHFV005	Goodfellow forest	glenian	1990
LHFV006	Willmott woods	Hannahland	2019
LHFV007	Outer otooles	Inis Áine	2005
LHFV008	Outer otooles	Inis Áine	1992
LHFV009	Lomanland	CENTRE	2005
LHFV010	Mylona marsh	Elliville	1990

3. Sequence length distribution

Distribution of sequence lengths across all input FASTA files. If a minimum length threshold is specified, it will be shown in the plot.

4. Metadata description

Unique locations: 19

Date range: 1982 → 2026-02-28

Date distribution by location.

5. Filtered sequences

The following sequences failed the length or N-content filters and will not be present in the output FASTA file:

6. Final dataset

7. Metadata issues

No metadata issues detected.