TB-Profiler result

Run: ERR2433008

Summary

Run ID: ERR2433008

Sample name:

Date: 31-03-2023 18:11:58

Number of reads: 576775

Percentage reads mapped: 99.6

Strain: lineage4.1.1.3

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
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
ald 3087278 c.464delG frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.95 ethionamide
ethA 4326604 c.869dupA frameshift_variant 1.0 ethionamide, ethionamide
gid 4407898 c.304delC frameshift_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8334 p.Met345Val missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.23
rpoB 762285 p.Arg827Cys missense_variant 1.0
rpoC 763733 p.Pro122Ser missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775775 c.2706G>A synonymous_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.13
rrs 1473104 n.1259C>A non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103207 c.-165C>T upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289538 c.-297G>C upstream_gene_variant 0.11
eis 2715083 c.248_249dupGT frameshift_variant 1.0
thyX 3067430 c.516C>A synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038847 p.Ser620Pro missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268937 c.-101T>C upstream_gene_variant 0.12
aftB 4269555 c.-719C>T upstream_gene_variant 0.13
ethA 4326243 p.Asp411Asn missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0