GS_004ZWZ2.1

Display Name: USA/GS_004ZWZ2.1/2025-02-25

Rothstein, A. P.; Collins, S.; Muir, G.; Qiu, X.; Simas, A.; Lu, B.; Cosca, B.; Girinathan, B.; Leeson, P.; Philipson, C. W.; Plocik, A. M.; Simen, B.

Submission details

Submission ID

PV271596.1.seg1/PV271595.1.seg3/PV271591.1.seg4/PV271594.1.seg5/PV271593.1.seg6/PV271592.1.seg7

Submitting group

Automated Ingest from INSDC/NCBI Virus by Loculus

Date submitted

2025-04-03 08:01:46 UTC

Date released

2025-04-03 10:18:30 UTC

Authors

Author affiliations

Ginkgo Bioworks, Ginkgo Biosecurity

Clade

Clade HA

6B.1A.5a.2a

Clade NA

C.5.3.1

Alignment states and QC metrics seg1

Completeness seg1

100.00%

Length seg1

2318

Total ambiguous nucs seg1

Total deleted nucs seg1

Total frame shifts seg1

Total inserted nucs seg1

Total SNPs seg1

Total unknown nucs seg1

Alignment states and QC metrics seg3

Completeness seg3

100.00%

Length seg3

2208

Total ambiguous nucs seg3

Total deleted nucs seg3

Total frame shifts seg3

Total inserted nucs seg3

Total SNPs seg3

Total unknown nucs seg3

Alignment states and QC metrics seg4

Completeness seg4

100.00%

Length seg4

1763

Total ambiguous nucs seg4

Total deleted nucs seg4

Total frame shifts seg4

Total inserted nucs seg4

Total SNPs seg4

100

Total unknown nucs seg4

Alignment states and QC metrics seg5

Completeness seg5

100.00%

Length seg5

1542

Total ambiguous nucs seg5

Total deleted nucs seg5

Total frame shifts seg5

Total inserted nucs seg5

Total SNPs seg5

Total unknown nucs seg5

Alignment states and QC metrics seg6

Completeness seg6

100.00%

Length seg6

1433

Total ambiguous nucs seg6

Total deleted nucs seg6

Total frame shifts seg6

Total inserted nucs seg6

Total SNPs seg6

Total unknown nucs seg6

Alignment states and QC metrics seg7

Completeness seg7

100.00%

Length seg7

1002

Total ambiguous nucs seg7

Total deleted nucs seg7

Total frame shifts seg7

Total inserted nucs seg7

Total SNPs seg7

Total unknown nucs seg7

Sample details

Collection country

USA

Collection subdivision level 1

New York

Collection date

2025-02-25

Isolate name

GKISBBBE57592

Host

Host name scientific

Homo sapiens

Host taxon id

9606

INSDC

INSDC accession seg1

INSDC accession seg3

INSDC accession seg4

INSDC accession seg5

INSDC accession seg6

INSDC accession seg7

NCBI release date

2025-03-13

INSDC seg4

Subtype seg4

INSDC seg6

Subtype seg6

Nucleotide mutations

Mutations called relative to the NC_026438.1, NC_026435.1, NC_026437.1, CY121680.1, NC_026436.1, MW626056.1, NC_026431.1 & NC_026432.1 references

Substitutions

seg1

seg1:A18G

seg1:G25A

seg1:A90C

seg1:A96G

seg1:A108G

seg1:A132G

seg1:A138G

seg1:G161A

seg1:A174G

seg1:G198A

seg1:T201C

seg1:C242T

seg1:A243G

seg1:C285A

seg1:A291G

seg1:C309T

seg1:G375A

seg1:A441G

seg3

seg3:G40A

seg3:R53A

seg3:T81C

seg3:G84C

seg3:A88G

seg3:C90T

seg3:C99T

seg3:A114T

seg3:G126A

seg3:C153T

seg3:C162T

seg3:C165T

seg3:G170T

seg3:G187A

seg3:G204A

seg3:G298A

seg3:G423A

seg3:G477A

seg4

seg4:C42A

seg4:A47G

seg4:G57A

seg4:C64T

seg4:A119G

seg4:T161C

seg4:C164T

seg4:G188A

seg4:G221A

seg4:A231C

seg4:T276C

seg4:C293A

seg4:G311A

seg4:G322A

seg4:G338T

seg4:G360A

seg4:G416A

seg4:A429G

seg5

seg5:A33G

seg5:G42T

seg5:C87T

seg5:A97G

seg5:C141A

seg5:A165G

seg5:C171T

seg5:T177C

seg5:C180T

seg5:C249A

seg5:A288C

seg5:G298A

seg5:G309A

seg5:T314C

seg5:G315A

seg5:R341A

seg5:T365A

seg5:C378A

seg6

seg6:A144G

seg6:G163A

seg6:C434T

seg6:C452A

seg6:A590G

seg6:G607A

seg6:G623A

seg6:A785G

seg6:T799C

seg6:A818G

seg6:C893T

seg6:G914T

seg6:T1016C

seg6:A1049G

seg6:C1187T

seg6:A1193G

seg6:G1365A

seg6:T1403C

seg6:G1415T

seg7

seg7:G75A

seg7:C124A

seg7:G238A

seg7:G258A

seg7:A293G

seg7:G306A

seg7:G339A

seg7:G342A

seg7:C375A

seg7:T432C

seg7:G441T

seg7:G492A

seg7:C507A

seg7:A574G

seg7:C622A

seg7:G660A

seg7:T663C

seg7:G687A

Deletions

None

Insertions

ins_seg7:0:TAGATGTTTAAAG, ins_seg7:982:AAAACTA, ins_seg5:1497:AGAAAAATAC, ins_seg5:0:GGGTAGATAATCACTCAATGAGTGACATCGAAGCC, ins_seg3:0:TACTGATCCAAA, ins_seg3:2151:TTGTGGCAATGCTACTATTTGCTATCCATATTGTCCAAAAAAGTA, ins_seg4:0:GCGAAAGCAGG, ins_seg1:2280:TGTCGAATTGTTTAAAAACGA, ins_seg1:0:GGTCAAATATATTCAAT

Amino acid mutations

Mutations called relative to the NC_026438.1, NC_026435.1, NC_026437.1, CY121680.1, NC_026436.1, MW626056.1, NC_026431.1 & NC_026432.1 references

Substitutions

HA1

HA1:K54Q

HA1:S69P

HA1:S74R

HA1:S84N

HA1:D97N

HA1:T120A

HA1:N129D

HA1:K130N

HA1:P137S

HA1:N156K

HA1:L161I

HA1:S162N

HA1:K163Q

HA1:S164T

HA1:I166V

HA1:K169Q

HA1:S183P

HA1:S185I

HA2

HA2:E47K

HA2:I91V

HA2:S124N

HA2:F138V

HA2:E172K

HA2:E179D

HA2:I183T

M1

M1:L42I

M1:V80I

M1:K98R

M1:M192V

M1:Q208K

M1:K230R

M2

M2:D21G

M2:S23N

NA

NA:I46V

NA:S52N

NA:S200N

NA:I264T

NA:V453M

NA:K469N

NP

NP:E14D

NP:I33V

NP:V100I

NP:M105T

NP:X114E

NP:L122Q

NP:I136L

NP:V217I

NP:V425I

NP:S498N

PA

PA:V14I

PA:X18E

PA:I30V

PA:R57L

PA:V63I

PA:V100I

PA:P224S

PA:S225C

PA:R262K

PA:N321K

PA:I330V

PA:A337T

PA:K339N

PA:R362K

PA:I428L

PA:I438V

PA:I505V

PA-X

PA-X:V14I

PA-X:X18E

PA-X:I30V

PA-X:R57L

PA-X:V63I

PA-X:V100I

PA-X:R199K

PA-X:N204S

PA-X:R206K

PA-X:R221Q

PA-X:L229S

PB2

PB2:D9N

PB2:R54K

PB2:M66I

PB2:T81M

PB2:D195N

PB2:G225S

PB2:R293K

PB2:R299K

PB2:V344M

PB2:I354L

PB2:S453T

PB2:L475M

PB2:V667I

PB2:V731I

SigPep

SigPep:L8M

SigPep:A13T

SigPep:A15V

Deletions

None

Insertions

None