GS_00DCQDF.1

Display Name: USA/GS_00DCQDF.1/2025-03-10
Rothstein, A. P.; Collins, S.; Muir, G.; Simas, A.; Lu, B.; Cosca, B.; Girinathan, B.; Leeson, P.; Philipson, C. W.; Plocik, A. M.; Simen, B.

Submission details

Submission ID
PV543888.1.seg1/PV543889.1.seg2/PV543884.1.seg4/PV543887.1.seg5/PV543886.1.seg6/PV543885.1.seg7
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-18 21:10:37 UTC
Date released
2025-04-18 21:10:49 UTC

Authors

Author affiliations
Ginkgo Bioworks, Ginkgo Biosecurity

Clade

Clade HA
V1A.3a.2
Clade NA
B.7.3

Alignment states and QC metrics seg4

Completeness seg4
99.20%
Length seg4
1861
Total ambiguous nucs seg4
0
Total deleted nucs seg4
9
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
54
Total unknown nucs seg4
0

Alignment states and QC metrics seg5

Completeness seg5
100.00%
Length seg5
1829
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
79
Total SNPs seg5
30
Total unknown nucs seg5
0

Alignment states and QC metrics seg6

Completeness seg6
100.00%
Length seg6
1542
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
141
Total SNPs seg6
33
Total unknown nucs seg6
0

Alignment states and QC metrics seg7

Completeness seg7
100.00%
Length seg7
1175
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
28
Total SNPs seg7
14
Total unknown nucs seg7
0

Sample details

Collection country
USA
Collection subdivision level 1
New York
Collection date
2025-03-10
Isolate name
GKISBBBE48588

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession seg1
PV543888.1
INSDC accession seg2
PV543889.1
INSDC accession seg4
PV543884.1
INSDC accession seg5
PV543887.1
INSDC accession seg6
PV543886.1
INSDC accession seg7
PV543885.1
NCBI release date
2025-04-18

Alignment states and QC metrics seg1

Length seg1
2355

Alignment states and QC metrics seg2

Length seg2
2384

INSDC seg4

Lineage seg4
vic

Nucleotide mutations

Mutations called relative to the CY115157.1, CY115158.1, CY115156.1, KX058884.1, CY115154.1, CY073894.1, CY115152.1 & CY115155.1 references

Substitutions

seg4

  • seg4:T195C
  • seg4:C252A
  • seg4:C265T
  • seg4:C270T
  • seg4:G297A
  • seg4:G312T
  • seg4:A318G
  • seg4:A351G
  • seg4:C375T
  • seg4:C378T
  • seg4:T402C
  • seg4:A427G
  • seg4:C441T
  • seg4:T444C
  • seg4:G457A
  • seg4:A461G
  • seg4:A463G
  • seg4:A484G

    • seg5

  • seg5:C3T
  • seg5:T46C
  • seg5:A55G
  • seg5:C178T
  • seg5:A224G
  • seg5:A235G
  • seg5:C271T
  • seg5:T298C
  • seg5:C313T
  • seg5:G361A
  • seg5:A373G
  • seg5:C380T
  • seg5:A454G
  • seg5:A478T
  • seg5:C523T
  • seg5:C608T
  • seg5:A763G
  • seg5:C841T

    • seg6

  • seg6:T9C
  • seg6:C125A
  • seg6:C140T
  • seg6:C143T
  • seg6:T212C
  • seg6:A358G
  • seg6:T363C
  • seg6:C394T
  • seg6:C399T
  • seg6:A504G
  • seg6:C519T
  • seg6:C591T
  • seg6:A660C
  • seg6:T714A
  • seg6:C849T
  • seg6:T879C
  • seg6:T885G
  • seg6:A894C

    • seg7

  • seg7:C33T
  • seg7:C46T
  • seg7:A83G
  • seg7:T125A
  • seg7:G316A
  • seg7:A419G
  • seg7:G482A
  • seg7:G500T
  • seg7:G521A
  • seg7:G536A
  • seg7:C656T
  • seg7:T772C
  • seg7:A919G
  • seg7:A967G
    • Deletions
    seg4:562-570
    Insertions
    ins_seg7:0:CAGGCACTTTCTTA, ins_seg7:1147:AAAAGTGCGTTGTT, ins_seg6:0:ATCTTCTCAAAACTGAAGCAAATAGGCCAAAAATGAACA, ins_seg6:1401:TGGGAGAATGGTTAAGTTTGTTCTAAACCCTTTGTTCCTATTTTATTTGAACAATTGTCCTTGCTAAACTTAATTGTTTCTGAAAAATCCTCTTGTTACTAC, ins_seg5:0:ATTTTCTTGTGAACTCCA, ins_seg5:1750:CGTTTGGAATATGGGTGTTTATTCTCATTAAAATAAATATAAAAAATGCTGTTGTTTCTAC

    Amino acid mutations

    Mutations called relative to the CY115157.1, CY115158.1, CY115156.1, KX058884.1, CY115154.1, CY073894.1, CY115152.1 & CY115155.1 references

    Substitutions

    HA1

  • HA1:I117V
  • HA1:A127T
  • HA1:E128G
  • HA1:N129D
  • HA1:K136E
  • HA1:P144L
  • HA1:N150K
  • HA1:E183K
  • HA1:G184E
  • HA1:N197E
  • HA1:A199T
  • HA1:K203R
  • HA1:R279K

    • M1

  • M1:T15I
  • M1:R105K

    • NA

  • NA:P42Q
  • NA:A47V
  • NA:P48L
  • NA:V71A
  • NA:I120V
  • NA:K220N
  • NA:S295R
  • NA:N340D
  • NA:K343E
  • NA:E358K
  • NA:G378E
  • NA:D384G
  • NA:A395V
  • NA:V401I

    • NP

  • NP:I9M
  • NP:T66A
  • NP:V453A
    • Deletions
    HA1:162-164
    Insertions
    None