TB-Profiler result

Run: SRR22251329
Summary

Run ID: SRR22251329

Sample name:

Date: 10-02-2024 08:01:43

Number of reads: 2156394

Percentage reads mapped: 97.72

Strain: lineage2.1

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R gid c.102delG (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.1 East-Asian (non-Beijing) None None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7963 p.Gly221Glu missense_variant 0.15
gyrA 7970 c.669T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491232 c.450T>C synonymous_variant 0.16
fgd1 491259 c.477T>C synonymous_variant 0.22
fgd1 491268 c.486C>T synonymous_variant 0.19
fgd1 491286 c.504G>C synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760718 c.912C>T synonymous_variant 0.17
rpoB 760724 c.918T>C synonymous_variant 0.16
rpoB 762813 p.Met1003Val missense_variant 0.15
rpoC 762818 c.-552C>G upstream_gene_variant 0.14
rpoC 762857 c.-513C>G upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763900 c.531G>C synonymous_variant 0.15
rpoC 764716 c.1347G>C synonymous_variant 0.16
rpoC 764752 c.1383G>C synonymous_variant 0.18
rpoC 764764 c.1395T>C synonymous_variant 0.18
rpoC 764803 c.1434C>T synonymous_variant 0.23
rpoC 764809 c.1440C>T synonymous_variant 0.23
rpoC 764812 c.1443C>G synonymous_variant 0.23
rpoC 764815 c.1446A>G synonymous_variant 0.21
rpoC 764824 c.1455T>C synonymous_variant 0.22
rpoC 764833 c.1464A>G synonymous_variant 0.19
rpoC 764836 c.1467G>A synonymous_variant 0.19
rpoC 764842 c.1473C>T synonymous_variant 0.2
rpoC 764869 c.1500C>T synonymous_variant 0.15
rpoC 765121 c.1752G>A synonymous_variant 0.93
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.24
rpoC 767059 c.3690T>G synonymous_variant 0.22
rpoC 767062 c.3693C>A synonymous_variant 0.22
rpoC 767098 c.3729T>C synonymous_variant 0.22
rpoC 767119 c.3750A>G synonymous_variant 0.17
rpoC 767134 c.3765C>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778706 p.Val67Gly missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781832 c.273T>C synonymous_variant 0.16
rpsL 781865 c.306G>C synonymous_variant 0.16
rpsL 781868 c.309T>C synonymous_variant 0.19
rpsL 781871 c.312G>C synonymous_variant 0.17
rpsL 781892 c.333A>G synonymous_variant 0.18
rpsL 781898 c.339A>T synonymous_variant 0.17
rpsL 781904 c.345C>T synonymous_variant 0.17
rpsL 781907 c.348T>C synonymous_variant 0.17
rpsL 781916 c.357T>G synonymous_variant 0.18
rpsL 781929 p.Gly124Ser missense_variant 0.21
fbiC 1304443 p.Ala505Thr missense_variant 1.0
embR 1417272 p.Thr26Pro missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833802 c.261A>G synonymous_variant 0.17
rpsA 1833811 c.270G>T synonymous_variant 0.17
rpsA 1833817 c.276C>G synonymous_variant 0.16
rpsA 1833820 c.279G>A synonymous_variant 0.17
rpsA 1833856 c.315A>G synonymous_variant 0.17
rpsA 1833859 c.318C>T synonymous_variant 0.17
rpsA 1833874 c.333T>C synonymous_variant 0.16
rpsA 1833894 p.Ala118Glu missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834297 c.756C>G synonymous_variant 0.19
rpsA 1834303 c.762T>G synonymous_variant 0.19
rpsA 1834306 c.765T>C synonymous_variant 0.19
rpsA 1834348 c.807T>C synonymous_variant 0.17
rpsA 1834366 c.825A>G synonymous_variant 0.18
rpsA 1834369 c.828C>G synonymous_variant 0.18
rpsA 1834396 c.855G>C synonymous_variant 0.17
rpsA 1834451 c.910T>C synonymous_variant 0.17
rpsA 1834456 c.915T>G synonymous_variant 0.17
rpsA 1834459 c.918G>C synonymous_variant 0.17
rpsA 1834468 c.927A>G synonymous_variant 0.16
rpsA 1834499 c.958C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918306 p.Arg123Ser missense_variant 1.0
katG 2153961 c.2151G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518902 p.Ala263Val missense_variant 0.97
folC 2747026 c.573C>G synonymous_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641110 p.Ala190Thr missense_variant 1.0
clpC1 4040841 c.-138delG upstream_gene_variant 1.0
embC 4240418 p.Gly186Cys missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246088 c.-426A>G upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0