TB-Profiler result

Run: ERR7911634
Summary

Run ID: ERR7911634

Sample name:

Date: 19-10-2023 13:31:02

Number of reads: 3151575

Percentage reads mapped: 99.67

Strain: lineage4.4.1.1;lineage2.2.1

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (0.14), inhA p.Ser94Ala (0.91), katG p.Ser315Thr (0.89)
Ethambutol R embB p.Met306Val (0.13), embB p.Gln497Arg (0.91)
Pyrazinamide R pncA p.Gln10Pro (0.85)
Streptomycin
Fluoroquinolones R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Tyr (0.79)
Moxifloxacin R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Tyr (0.79)
Ofloxacin R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Tyr (0.79)
Levofloxacin R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Tyr (0.79)
Ciprofloxacin R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Tyr (0.79)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.81)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.14), inhA p.Ser94Ala (0.91), ethA c.65delA (0.21), ethA c.65delA (0.21), ethR p.Ala95Thr (0.16)
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 0.13
lineage4 Euro-American LAM;T;S;X;H None 0.91
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.14
lineage4.4 Euro-American S;T None 0.87
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.08
lineage4.4.1 Euro-American (S-type) S;T None 0.88
lineage4.4.1.1 Euro-American S;Orphans None 0.85
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 7572 p.Ser91Pro missense_variant 0.23 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Tyr missense_variant 0.79 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.14 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 0.91 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.89 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 0.85 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.81 kanamycin
embB 4247429 p.Met306Val missense_variant 0.13 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.91 ethambutol
ethA 4327408 c.65delA frameshift_variant 0.21 ethionamide, ethionamide
ethR 4327831 p.Ala95Thr missense_variant 0.16 ethionamide
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 8164 p.Ala288Asp missense_variant 0.14
gyrA 9138 p.Gln613Glu missense_variant 0.82
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.19
mshA 575907 p.Ala187Val missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.14
rpoC 763555 c.186C>T synonymous_variant 0.17
rpoC 764931 p.Ala521Asp missense_variant 0.14
rpoC 764936 p.Gln523Glu missense_variant 0.85
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.18
mmpL5 776182 p.Asp767Asn missense_variant 0.12
mmpL5 777416 c.1065G>T synonymous_variant 0.87
mmpS5 778979 c.-74G>T upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475954 n.2297A>C non_coding_transcript_exon_variant 0.88
rpsA 1833585 p.Asp15Gly missense_variant 0.84
rpsA 1834177 c.636A>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.85
PPE35 2167926 p.Leu896Ser missense_variant 0.14
PPE35 2168479 p.Thr712Pro missense_variant 0.84
PPE35 2169840 p.Gly258Asp missense_variant 0.88
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065039 p.Tyr385Asp missense_variant 0.79
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.9
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.79
Rv3236c 3612665 p.Val151Ala missense_variant 0.84
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.18
gid 4407790 p.Ala138Glu missense_variant 0.83
gid 4407927 p.Glu92Asp missense_variant 0.18