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_000PY5D.1

India/LOC_000PY5D.1/2019
R. R. Sahay, S. Dhandore, A. Chauhan, L. Bhatt, V. Garg, N. Gupta, D. A. Nyayanit, A. M. Shete, R. Singh, S. Patil, H. Sharma, D. Meena, P. Gawande, K. Kalele, R. Jain, D. Mali, B. Malhotra, V. Nag, H. Kaur, N. Singh, S. Singh, M. Gopalkrishnan, P. D. Yadav & P. Yadav

National Institute of Virology, Maximum Containment Laboratory

Sample details

Collection date
2019
Earliest release date
2020-11-13
Sampling location
India (Gujarat State)
Isolate name
MCL-19-H-2028

Data use terms

Data use terms
OPEN
Data use terms URL

INSDC

NCBI release date
2020-11-13
INSDC accession L segment
INSDC accession M segment
INSDC accession S segment

Host

Host

Submission details

Submission ID
MN866175.1.L/MN866174.1.M/MN866176.1.S
Submitting group
Date submitted
2026-07-22 16:51:12 UTC
Date released
2026-07-22 16:55:04 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 M segment
341
Total inserted nucs M segment
4
Length M segment
5330 (97.6%)
Total SNPs L segment
1631
Total inserted nucs L segment
17
Total unknown nucs L segment
58
Length L segment
12102 (99.3%)
Total SNPs S segment
211
Length S segment
1600 (88.6%)

Nucleotide mutations

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

Substitutions

L segment

  • A35G
  • G43C
  • C48T
  • T49C
  • C59T
  • C63T
  • C64G
  • T66C
  • G71T
  • A72T
  • C85T
  • G93A
  • A109G
  • G112A
  • T121C
  • T131A
  • C136T
  • T139C

M segment

  • G51A
  • A53G
  • G65A
  • G72A
  • T78C
  • A97G
  • A127G
  • C133T
  • G145A
  • T148C
  • A149C
  • C151T
  • C155T
  • G166A
  • A171G
  • T181A
  • C185G
  • A204G

S segment

  • T16A
  • C31G
  • T32C
  • G34A
  • A38G
  • A45G
  • C48T
  • A84G
  • A98T
  • A102G
  • C126T
  • T141C
  • C150T
  • G153A
  • T166C
  • A173G
  • C183T
  • A186G
Deletions
N/A
Insertions

L segment

ins_66:C, ins_11931:AT, ins_12108:TACCTTTCATTTCA

M segment

ins_5062:GGG, ins_5166:A

Amino acid substitutions

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

Substitutions

GPC

  • GPC:I3M
  • GPC:N21H
  • GPC:P23S
  • GPC:E28G
  • GPC:N31K
  • GPC:H33D
  • GPC:D39G
  • GPC:P47L
  • GPC:V54F
  • GPC:S64T
  • GPC:P66L
  • GPC:G69R
  • GPC:V76P
  • GPC:S80P
  • GPC:I82A
  • GPC:P96L
  • GPC:V102I
  • GPC:V103I

NP

  • NP:Y20F
  • NP:K45R
  • NP:D116E
  • NP:N150H
  • NP:Q179L
  • NP:D199E
  • NP:R270K
  • NP:S275N
  • NP:R428K

RdRp

  • RdRp:S6N
  • RdRp:S19T
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:S67V
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:L90I
  • RdRp:I114V
  • RdRp:I157M
  • RdRp:T163V
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:V214I
  • RdRp:K275R
Deletions
N/A
Insertions

GPC

ins_GPC:1658:G

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