TB-Profiler result

Run: ERR1034911
Summary

Run ID: ERR1034911

Sample name:

Date: 20-10-2023 23:25:33

Number of reads: 6581217

Percentage reads mapped: 99.01

Strain: lineage4.3.4.2;lineage4.3.3

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.Gln432Glu (0.57), rpoB p.Asp435Val (0.56), rpoB p.Ser450Leu (0.49)
Isoniazid R fabG1 c.-15C>T (0.45), inhA p.Ile194Thr (0.56), katG p.Ser315Thr (0.52), ahpC c.-48G>A (0.44)
Ethambutol R embB p.Met306Val (0.51), embB p.Met423Thr (0.48)
Pyrazinamide R pncA c.389_390insA (0.42), pncA c.389_390insA (0.42), pncA p.Val125Gly (0.56)
Streptomycin R gid p.Ala80Pro (0.54)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.45), inhA p.Ile194Thr (0.56)
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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.49
lineage4.3.4 Euro-American (LAM) LAM RD174 0.51
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.52
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 761100 p.Gln432Glu missense_variant 0.57 rifampicin
rpoB 761110 p.Asp435Val missense_variant 0.56 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.49 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.45 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 0.56 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.52 isoniazid
pncA 2288852 c.389_390insA frameshift_variant 0.42 pyrazinamide, pyrazinamide
pncA 2288868 p.Val125Gly missense_variant 0.56 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.44 isoniazid
embB 4247429 p.Met306Val missense_variant 0.51 ethambutol
embB 4247781 p.Met423Thr missense_variant 0.48 ethambutol
gid 4407965 p.Ala80Pro missense_variant 0.54 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
gyrB 6140 p.Val301Leu missense_variant 0.53
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.51
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490655 c.-128T>C upstream_gene_variant 0.47
mshA 576160 c.813C>T synonymous_variant 0.5
rpoC 764817 p.Val483Gly missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800990 p.Lys61Thr missense_variant 0.37
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.11
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.13
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.12
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.1
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.1
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.1
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.1
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.11
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.11
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.11
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.11
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.11
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.12
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.13
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.11
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.12
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289743 c.-502A>G upstream_gene_variant 0.17
kasA 2518919 p.Gly269Ser missense_variant 0.48
thyX 3067954 c.-9G>A upstream_gene_variant 0.5
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.45
alr 3840719 c.702A>G synonymous_variant 0.52
rpoA 3877586 p.Leu308Phe missense_variant 0.47
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328127 c.-654C>G upstream_gene_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408027 p.Leu59Arg missense_variant 0.52
gid 4408156 p.Leu16Arg missense_variant 1.0