TB-Profiler result

Run: ERR10748150

Summary

Run ID: ERR10748150

Sample name:

Date: 31-03-2023 10:45:46

Number of reads: 466591

Percentage reads mapped: 99.84

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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288827 p.Val139Met missense_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326876 c.597delC frameshift_variant 1.0 ethionamide, 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 5070 c.-170C>T upstream_gene_variant 0.2
gyrB 6115 p.Gln292His missense_variant 0.25
gyrB 6608 p.Val457Leu missense_variant 1.0
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 490657 c.-126T>C upstream_gene_variant 0.12
fgd1 490967 p.Gly62Asp missense_variant 0.12
ccsA 620187 c.297C>A synonymous_variant 0.11
rpoB 763110 p.Lys1102* stop_gained 0.29
rpoB 763147 p.Ser1114Leu missense_variant 0.25
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778285 p.Pro66Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801354 c.546G>A synonymous_variant 1.0
fbiC 1303404 c.474A>G synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674321 c.120G>T synonymous_variant 0.29
rpsA 1834583 p.Val348Leu missense_variant 0.11
rpsA 1834856 p.Glu439* stop_gained 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102258 p.Ser262Cys missense_variant 0.11
katG 2154087 c.2025C>T synonymous_variant 0.12
katG 2154308 p.Asn602His missense_variant 0.13
katG 2155469 p.Asp215Tyr missense_variant 0.18
katG 2156266 c.-155G>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859596 p.Ala275Thr missense_variant 0.11
pepQ 2860223 p.Ser66Pro missense_variant 1.0
ald 3086713 c.-107C>A upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449616 p.Met371Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840353 c.1068T>C synonymous_variant 0.12
rpoA 3877692 c.816G>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.96
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4328245 c.-772C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0