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_00D99W1.1

USA/LOC_00D99W1.1/2026-09-06
A. P. Rothstein, G. Muir, A. Simas, A. Sum, B. Girinathan, P. Leeson & D. Gratalo

Perimeter, Bioinformatics

Sample details

Collection date
2026-09-06
Earliest release date
2026-09-22
Sampling location
USA (New York)
Isolate name
SARS-CoV-2/human/USA/JFK-GKISBBBJ51113/2026

Data use terms

Data use terms
OPEN
Data use terms URL

INSDC

NCBI release date
2026-09-22
NCBI update date
2026-09-22
INSDC accession
BioProject accession
BioSample accession
Raw reads accession

Host

Host

Submission details

Submission ID
QB045815.1
Submitting group
Date submitted
2026-09-28 21:13:44 UTC
Date released
2026-09-28 21:46:02 UTC

Lineage

Nextstrain clade
25I
Pango lineage
SQ.3

Alignment and QC

Total SNPs
141
Total inserted nucs
13
Total deleted nucs
68
Total unknown nucs
923
Total frame shifts
1
Frame shifts
ORF6:62(nt:27385-27387)
Length
29807 (96.8%)

Nucleotide mutations

Mutations called relative to the MN908947.3 reference

Substitutions
  • C193T
  • C241T
  • C313T
  • C635T
  • T670G
  • C832T
  • G1043A
  • C2037T
  • G2281T
  • G2731A
  • C3037T
  • A3309G
  • T4159C
  • G4184A
  • C4321T
  • T4579A
  • C5884T
  • C5907T
Deletions
515-523, 11288-11296, 21765-21770, 22194-22196, 22289-22294, 28362-28370, 29734-29759
Insertions
ins_22204:GCTTCAGACACT, ins_27384:C

Amino acid substitutions

Substitutions called relative to the MN908947.3 reference

Substitutions

E

  • E:T9I
  • E:T11A

M

  • M:Q19E
  • M:A63T
  • M:V66L

N

  • N:P13L
  • N:T49I
  • N:A173V
  • N:R203K
  • N:G204R
  • N:Q241H
  • N:S413R

ORF1a

  • ORF1a:R124C
  • ORF1a:S135R
  • ORF1a:A260T
  • ORF1a:A591V
  • ORF1a:K672N
  • ORF1a:E1015G
  • ORF1a:G1307S
  • ORF1a:T1881I
  • ORF1a:V2071F
  • ORF1a:S2303F
  • ORF1a:I2332V
  • ORF1a:T3090I
  • ORF1a:T3255I
  • ORF1a:P3395H
  • ORF1a:A3657V
  • ORF1a:I3944L

ORF1b

  • ORF1b:P314L
  • ORF1b:I527T
  • ORF1b:I1566V
  • ORF1b:T1896I

ORF3a

  • ORF3a:A59S
  • ORF3a:A72T
  • ORF3a:A103S
  • ORF3a:G174D
  • ORF3a:T223I

ORF6

  • ORF6:D61H

ORF9b

  • ORF9b:P10S

S

  • S:P9L
  • S:R21T
  • S:P26L
  • S:A67V
  • S:T95I
  • S:I101T
  • S:F157S
  • S:N164K
  • S:S172F
  • S:K187T
  • S:L212I
  • S:P251S
  • S:I326V
  • S:G339Y
  • S:A348P
  • S:K356T
  • S:S371F
  • S:S373P
Deletions

N

N:31-33

ORF1a

ORF1a:84-86, ORF1a:3675-3677

ORF9b

ORF9b:27-29

S

S:69, S:70, S:211, S:242, S:243
Insertions

S

ins_S:214:ASDT

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