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_000S5ZB.1

Pakistan/LOC_000S5ZB.1/1965
J. W. Koehler, K. L. Delp, B. J. Kearney, T. A. Conrad, R. J. Schoepp, A. R. Garrison, L. A. Altimura, C. A. Rossi & T. D. Minogue

USAMRIID, DSD

Sample details

Collection date
1965
Earliest release date
2017-04-02
Sampling location
Pakistan
Isolate name
UCCR4413

Data use terms

Data use terms
OPEN
Data use terms URL

INSDC

NCBI release date
2017-04-02
INSDC accession L segment
INSDC accession M segment
INSDC accession S segment

Host

Host

Submission details

Submission ID
KY484039.1.L/KY484038.1.M/KY484037.1.S
Submitting group
Date submitted
2026-08-05 15:16:45 UTC
Date released
2026-08-05 15:19:06 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
1635
Total inserted nucs L segment
60
Total deleted nucs L segment
1
Length L segment
12167 (100%)
Total SNPs S segment
221
Total inserted nucs S segment
16
Length S segment
1673 (91.7%)
Total SNPs M segment
1448
Total inserted nucs M segment
77
Total deleted nucs M segment
75
Total frame shifts M segment
2
Frame shifts M segment
GPC:15-33(nt:130-187),GPC:215-237(nt:730-799)
Length M segment
5326 (97.6%)

Nucleotide mutations

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

Substitutions

L segment

  • G23T
  • A35G
  • C37T
  • G43T
  • T49C
  • C63G
  • C64T
  • T65C
  • T66C
  • T68C
  • G69A
  • G71C
  • C85T
  • G88A
  • G93A
  • A109G
  • C117A
  • A124G

M segment

  • G34A
  • T35A
  • A38G
  • G46A
  • A47G
  • A48C
  • G51A
  • A53G
  • T54A
  • T55G
  • G56A
  • A57G
  • G58A
  • T63C
  • T64G
  • G65T
  • A66T
  • T67A

S segment

  • T16A
  • C31G
  • T63C
  • A65G
  • A84G
  • A93G
  • A98T
  • A102G
  • C150T
  • G153A
  • G155A
  • T156C
  • T166C
  • A173G
  • G174A
  • G180A
  • A186G
  • C192T
Deletions

L segment

12034

M segment

188-195, 230-250, 704-729, 5177-5196
Insertions

L segment

ins_58:T, ins_11917:CA, ins_12054:TACAATTTT, ins_12083:ACTATTC, ins_12096:GTTCATGTCCATTTTATTATTTCTGGGGTGTGGGGGGAACG

M segment

ins_0:TCTC, ins_129:ATATAAAGTTG, ins_463:ACTGAAAACAGTGAAAGCACAGACACA, ins_595:GGG, ins_799:GCACACTCAGAACGCTCTCAGCTGAA, ins_5059:GGG, ins_5226:TGT

S segment

ins_0:TCTCAAAGAAACACGT

Amino acid substitutions

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

Substitutions

GPC

  • GPC:M1L
  • GPC:H2Y
  • GPC:I3A
  • GPC:S4L
  • GPC:M6A
  • GPC:Y7S
  • GPC:V9I
  • GPC:F10L
  • GPC:C11H
  • GPC:L12Q
  • GPC:Q13H
  • GPC:I82A
  • GPC:T84A
  • GPC:K85N
  • GPC:G86R
  • GPC:L87T
  • GPC:S88T
  • GPC:L89Y

NP

  • NP:N9S
  • NP:Y20F
  • NP:S39N
  • NP:K45R
  • NP:V83A
  • NP:D116E
  • NP:A124S
  • NP:Q179L
  • NP:D199E
  • NP:K208M
  • NP:R270K
  • NP:A307V
  • NP:E322D
  • NP:Q405L
  • NP:R428K

RdRp

  • RdRp:S6N
  • RdRp:A14D
  • RdRp:S19T
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:S67V
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:I114V
  • RdRp:T163A
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:I223V
  • RdRp:K275R
  • RdRp:I279V
Deletions

GPC

GPC:34-60, GPC:206-214
Insertions

GPC

ins_GPC:94:STTPKSSTKPTTHIATAHLAESDGSGETTLLLPTTASQYTTEGQTSL, ins_GPC:175:T, ins_GPC:1661:K

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