TB-Profiler result

Run: ERR4799986
Summary

Run ID: ERR4799986

Sample name:

Date: 20-10-2023 03:36:13

Number of reads: 3098712

Percentage reads mapped: 99.52

Strain: lineage4.8;lineage2.2.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.40)
Ethambutol R embB p.Met306Val (0.34)
Pyrazinamide R pncA c.393dupC (0.33), pncA c.393dupC (0.33)
Streptomycin R rpsL p.Lys43Arg (0.44)
Fluoroquinolones R gyrA p.Ala90Val (0.37), gyrA p.Asp94Gly (0.46)
Moxifloxacin R gyrA p.Ala90Val (0.37), gyrA p.Asp94Gly (0.46)
Ofloxacin R gyrA p.Ala90Val (0.37), gyrA p.Asp94Gly (0.46)
Levofloxacin R gyrA p.Ala90Val (0.37), gyrA p.Asp94Gly (0.46)
Ciprofloxacin R gyrA p.Ala90Val (0.37), gyrA p.Asp94Gly (0.46)
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 0.37
lineage4 Euro-American LAM;T;S;X;H None 0.61
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.46
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.66
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.35
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
gyrA 7570 p.Ala90Val missense_variant 0.37 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.46 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 0.44 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.4 isoniazid
pncA 2288848 c.393dupC frameshift_variant 0.33 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.34 ethambutol
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 0.53
gyrA 9304 p.Gly668Asp missense_variant 0.51
fgd1 491742 c.960T>C synonymous_variant 0.71
mshA 575907 p.Ala187Val missense_variant 0.23
mshA 576347 p.Thr334Ala missense_variant 0.69
ccsA 620553 c.663T>C synonymous_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.47
rpoC 764817 p.Val483Ala missense_variant 0.42
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.55
mmpL5 776182 p.Asp767Asn missense_variant 0.56
mmpL5 778426 p.Ala19Pro missense_variant 0.5
mmpS5 779615 c.-710C>G upstream_gene_variant 0.39
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305438 c.2508C>T synonymous_variant 0.7
Rv1258c 1406760 c.580_581insC frameshift_variant 0.35
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.57
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.44
PPE35 2167926 p.Leu896Ser missense_variant 0.64
PPE35 2170574 c.39C>T synonymous_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.68
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.49
Rv3236c 3612813 p.Thr102Ala missense_variant 0.42
fbiB 3642641 c.1107G>A synonymous_variant 0.62
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.33
embB 4249757 p.Thr1082Ala missense_variant 0.37
aftB 4267647 p.Asp397Gly missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.44
gid 4407927 p.Glu92Asp missense_variant 0.37