TB-Profiler result

Run: ERR9806898
Summary

Run ID: ERR9806898

Sample name:

Date: 21-05-2023 04:46:00

Number of reads: 2771549

Percentage reads mapped: 99.7

Strain: lineage4.3.2.1

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 fabG1 c.-15C>T (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 5807 p.Val190Ile missense_variant 0.12
gyrA 6709 c.-593A>G upstream_gene_variant 0.18
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8015 p.Gln238His missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762904 p.Asp1033Gly missense_variant 0.12
rpoC 763979 p.Glu204* stop_gained 0.17
rpoC 764536 c.1170delC frameshift_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775779 p.Thr901Asn missense_variant 0.11
mmpL5 776704 c.1776_1777insCGTC frameshift_variant 0.15
mmpL5 777259 p.Leu408Met missense_variant 0.12
mmpL5 777312 p.Pro390His missense_variant 0.14
mmpS5 778669 p.Gln79His missense_variant 0.13
mmpR5 779192 p.Ser68Ile missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781573 p.Gln5Arg missense_variant 0.15
rplC 800774 c.-35C>T upstream_gene_variant 0.13
fbiC 1303611 c.681G>A synonymous_variant 0.11
fbiC 1303816 p.Arg296Ser missense_variant 0.13
Rv1258c 1406537 c.804C>T synonymous_variant 0.14
atpE 1460885 c.-160G>T upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475258 n.1601T>C non_coding_transcript_exon_variant 0.22
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.5
inhA 1674668 p.Pro156Gln missense_variant 0.15
inhA 1674729 c.528G>A synonymous_variant 0.15
rpsA 1834885 c.1344G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154819 c.1293C>A synonymous_variant 0.14
katG 2154940 p.Glu391Leu missense_variant 0.13
katG 2155912 p.Glu67Gly missense_variant 0.11
PPE35 2168432 c.2181G>T synonymous_variant 0.12
PPE35 2168869 p.Pro582Ser missense_variant 0.4
PPE35 2169398 c.1215C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289482 c.-241C>A upstream_gene_variant 0.13
pncA 2290126 c.-885C>A upstream_gene_variant 0.13
kasA 2518124 p.Pro4Ser missense_variant 0.12
kasA 2518149 p.Pro12His missense_variant 0.12
ahpC 2725962 c.-231C>T upstream_gene_variant 0.12
ahpC 2726054 c.-139C>T upstream_gene_variant 0.14
ahpC 2726201 c.9G>A synonymous_variant 0.13
Rv2752c 3065727 c.465C>A synonymous_variant 0.12
thyX 3067624 p.Tyr108His missense_variant 0.13
thyX 3068038 c.-93C>A upstream_gene_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448987 p.Arg162Trp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474404 p.Asn133Ser missense_variant 0.11
fprA 3474610 p.Pro202Thr missense_variant 0.14
fbiB 3642793 p.Pro420Gln missense_variant 0.12
ddn 3987168 p.Leu109Ile missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039067 c.1638G>T synonymous_variant 0.15
clpC1 4039796 c.909C>T synonymous_variant 0.12
clpC1 4040213 c.492T>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269448 p.Val129Ala missense_variant 0.12
ubiA 4269466 p.Asn123Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0