This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.

LOC_000P8WL.1

Display Name: Sudan/LOC_000P8WL.1/2015
H. Bower, M. El Karsany, M. Alzain, B. Gannon, R. Mohamed, I. Mahmoud, M. Eldegail, R. Taha, A. El Halawi, A. Osman, S. Mohamednour, A. Semper, B. Atkinson, D. P. Carter, S. Dowall, J. Furneaux, V. Graham, J. Mellors, J. Osborne, S. T. Pullan, G. S. Slack, T. Brooks, R. Hewson, N. J. Beeching, J. Whitworth, D. Bausch & T. E. Fletcher

Sample details

Collection date
2015
Collection date (lower bound)
2015-01-01
Collection date (upper bound)
2015-12-31
Earliest release date
2019-04-10
Collection country
Sudan
Collection subdivision level 1
Darfur

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-11-17 15:07insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
Public Health England, Genomics of Rare and Emerging Human Pathogens

INSDC

NCBI release date
2019-04-10
INSDC accession L
INSDC accession M
INSDC accession S

Host

Host taxon id
Host name scientific
Homo sapiens

Alignment and QC metrics L

Length L
12153
Total SNPs L
271
Total inserted nucs L
49
Total deleted nucs L
0
Total ambiguous nucs L
2
Total unknown nucs L
180
Total frame shifts L
0
Completeness L
98.46%

Alignment and QC metrics M

Length M
5359
Total SNPs M
158
Total inserted nucs M
0
Total deleted nucs M
0
Total ambiguous nucs M
1
Total unknown nucs M
185
Total frame shifts M
0
Completeness M
96.40%

Alignment and QC metrics S

Length S
1644
Total SNPs S
132
Total inserted nucs S
1
Total deleted nucs S
0
Total ambiguous nucs S
0
Total unknown nucs S
0
Total frame shifts S
0
Completeness S
98.27%

Submission details

Submission ID
MK442895.1.L/MK442894.1.M/MK442893.1.S
Submitting group
Date submitted
2025-11-17 15:07:21 UTC
Date released
2025-11-17 15:12:08 UTC

Lineage

Segment S Lineage
III

Files

Annotations

Nucleotide mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

Substitutions

L

  • L:T10C
  • L:A40G
  • L:T65C
  • L:T70C
  • L:G93A
  • L:T151C
  • L:C244T
  • L:T254A
  • L:C295T
  • L:A298G
  • L:C313T
  • L:T340C
  • L:C427T
  • L:C481T
  • L:A544G
  • L:T550G
  • L:G553A
  • L:C568T

    • M

  • M:A57G
  • M:A87G
  • M:G110A
  • M:C120T
  • M:T173C
  • M:G197A
  • M:C217T
  • M:C231T
  • M:T259C
  • M:C320T
  • M:T360C
  • M:A374G
  • M:A377G
  • M:T385C
  • M:C404T
  • M:T406C
  • M:C410T
  • M:G414A

    • S

  • S:G47C
  • S:A50G
  • S:G54A
  • S:G67A
  • S:G99A
  • S:G100A
  • S:C178A
  • S:T181C
  • S:G189A
  • S:T199C
  • S:G202A
  • S:G229A
  • S:C235T
  • S:C244T
  • S:A247G
  • S:G271A
  • S:C295T
  • S:A298G
    • Deletions
    None
    Insertions
    ins_L:12108:TTCATCGTCATCGTTATTATCTTGGGGTGTGGGGGGAACGATTTCTTTG, ins_S:1577:A

    Amino acid mutations

    Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

    Substitutions

    GPC

  • GPC:M6I
  • GPC:L10F
  • GPC:M35I
  • GPC:P42L
  • GPC:P47S
  • GPC:L56P
  • GPC:S90P
  • GPC:V98A
  • GPC:L105S
  • GPC:G108S
  • GPC:P112S
  • GPC:S121F
  • GPC:A122T
  • GPC:P123L
  • GPC:N131S
  • GPC:S171P
  • GPC:S180P
  • GPC:P214T

    • NP

  • NP:R15K
  • NP:R45K
  • NP:K91R
  • NP:T124A
  • NP:G125N
  • NP:L179Q
  • NP:H195R
  • NP:I246V
  • NP:S301G
  • NP:K428R
  • NP:V436I

    • RdRp

  • RdRp:S6N
  • RdRp:Y60N
  • RdRp:I505T
  • RdRp:T767A
  • RdRp:A775T
  • RdRp:I783T
  • RdRp:K809R
  • RdRp:G812E
  • RdRp:T876S
  • RdRp:A1038T
  • RdRp:G1047E
  • RdRp:V1228I
  • RdRp:F1279S
  • RdRp:N1367D
  • RdRp:M1647L
  • RdRp:P1660T
  • RdRp:T1675N
  • RdRp:R1676K
    • Deletions
    None
    Insertions
    None

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