TB-Profiler result

Run: ERR4813060
Summary

Run ID: ERR4813060

Sample name:

Date: 01-04-2023 12:30:47

Number of reads: 1107340

Percentage reads mapped: 99.54

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.45
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 7582 p.Asp94Gly missense_variant 0.41 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.61 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.56 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289099 p.Lys48Thr missense_variant 0.44 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.35 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 0.53 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 8040 p.Gly247Ser missense_variant 0.36
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575174 c.-174G>T upstream_gene_variant 0.12
mshA 576742 c.1395G>T synonymous_variant 0.12
rpoB 761889 p.Val695Leu missense_variant 0.52
rpoC 764995 c.1626C>G synonymous_variant 0.54
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779357 p.Arg123Met missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.6
rplC 801393 p.Lys195Asn missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
PPE35 2170182 p.Trp144Leu missense_variant 0.22
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.56
kasA 2519174 p.Glu354* stop_gained 0.2
eis 2714876 p.Ala153Pro missense_variant 0.14
folC 2747723 c.-125G>T upstream_gene_variant 0.12
ribD 2986708 c.-131G>T upstream_gene_variant 0.11
Rv2752c 3065517 c.675C>T synonymous_variant 0.56
Rv2752c 3066369 c.-178C>T upstream_gene_variant 0.15
thyX 3067695 p.Gly84Val missense_variant 0.12
thyX 3067774 p.Ala58Ser missense_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.6
ald 3086788 c.-32T>C upstream_gene_variant 0.53
ald 3087660 c.843dupC frameshift_variant 0.59
fbiD 3339050 c.-68C>A upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.41
fprA 3474299 p.Asp98Gly missense_variant 0.59
fbiB 3641613 p.Asp27Tyr missense_variant 0.12
rpoA 3878595 c.-88C>T upstream_gene_variant 0.29
clpC1 4038209 c.2496G>T synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.45
embC 4242182 p.Ala774Ser missense_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243392 p.Asn54Asp missense_variant 0.4
embA 4243793 c.561C>A synonymous_variant 0.22
aftB 4268435 c.402C>T synonymous_variant 0.12
ubiA 4269731 p.Ala35Ser missense_variant 0.74
ethA 4328317 c.-844C>T upstream_gene_variant 0.75
whiB6 4338266 c.256C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407986 p.Gly73Arg missense_variant 0.23
gid 4408156 p.Leu16Arg missense_variant 0.37