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_000SD7N.1

Sudan/LOC_000SD7N.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

Public Health England, Genomics of Rare and Emerging Human Pathogens

Sample details

Collection date
2015
Earliest release date
2019-04-10
Sampling location
Sudan (Darfur)
Isolate name
Sudan Darfur 2015

Data use terms

Data use terms
OPEN
Data use terms URL

INSDC

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

Host

Host

Submission details

Submission ID
MK442895.1.L/MK442894.1.M/MK442893.1.S
Submitting group
Date submitted
2026-10-01 11:42:04 UTC
Date released
2026-10-01 11:44:42 UTC

Clade & Lineage

Closest reference L segment
singleReference (variant)
Closest reference M segment
M (MH396653.1) (variant)
Closest reference S segment
S1 (OL774851.1) (variant)

Files

Annotations

Alignment and QC

Total SNPs L segment
271
Total inserted nucs L segment
49
Total ambiguous nucs L segment
2
Total unknown nucs L segment
180
Length L segment
12153 (98.5%)
Total SNPs M segment
677
Total ambiguous nucs M segment
1
Total unknown nucs M segment
185
Length M segment
5359 (94.8%)
Total SNPs S segment
30
Length S segment
1644 (91%)

Nucleotide mutations

Mutations called relative to the NC_005301.3, MH396653.1 & OL774851.1 references

Substitutions

L segment

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

M segment

  • A53G
  • G65A
  • T78C
  • T81C
  • C82T
  • A83G
  • G103A
  • G106A
  • G113A
  • T115C
  • C118T
  • T122C
  • G124A
  • A127G
  • C133T
  • A139G
  • G142A
  • A143G

S segment

  • T16A
  • A98T
  • T165C
  • C228T
  • A311G
  • G330A
  • C621T
  • A708T
  • G765A
  • G804A
  • G822A
  • T912C
  • A945C
  • A987G
  • C1035T
  • T1170C
  • A1314T
  • G1428A
Deletions
N/A
Insertions

L segment

ins_12108:TTCATCGTCATCGTTATTATCTTGGGGTGTGGGGGGAACGATTTCTTTG

Amino acid substitutions

Substitutions called relative to the NC_005301.3, MH396653.1 & OL774851.1 references

Substitutions

GPC

  • GPC:M6I
  • GPC:V9I
  • GPC:K19E
  • GPC:N21H
  • GPC:P23S
  • GPC:G26E
  • GPC:E28R
  • GPC:N31K
  • GPC:H33D
  • GPC:V34T
  • GPC:M35I
  • GPC:D39G
  • GPC:S41N
  • GPC:Q42L
  • GPC:P44S
  • GPC:P47S
  • GPC:P53S
  • GPC:V54I

NP

  • NP:Y20F
  • NP:K91R

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
N/A
Insertions
N/A

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