TB-Profiler result

Run: ERR229988
Summary

Run ID: ERR229988

Sample name:

Date: 19-10-2023 19:25:23

Number of reads: 3369964

Percentage reads mapped: 99.46

Strain: lineage4.2.1;lineage2.2.1

Drug-resistance: MDR-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 (0.99), rpoC p.Asp485Asn (0.91), rpoC p.Leu527Val (0.13)
Isoniazid R inhA c.-154G>A (0.92), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gln497Arg (0.88)
Pyrazinamide
Streptomycin R rpsL p.Lys88Arg (0.93)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R inhA c.-154G>A (0.92)
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 0.07
lineage4 Euro-American LAM;T;S;X;H None 0.93
lineage4.2 Euro-American H;T;LAM None 0.91
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.08
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.07
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.91
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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 0.91 rifampicin
rpoC 764948 p.Leu527Val missense_variant 0.13 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.93 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.92 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 0.88 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.91
fgd1 491742 c.960T>C synonymous_variant 0.12
ccsA 619969 p.Val27Ile missense_variant 0.84
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304253 c.1323G>T synonymous_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.97
ald 3086742 c.-78A>C upstream_gene_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.13
embB 4249594 c.3081G>A synonymous_variant 0.89
aftB 4267647 p.Asp397Gly missense_variant 0.13
ethA 4326314 p.Thr387Ile missense_variant 0.94
ethA 4328376 c.-903G>C upstream_gene_variant 0.91
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.13