TB-Profiler result

Run: ERR2516475

Summary

Run ID: ERR2516475

Sample name:

Date: 31-03-2023 21:33:23

Number of reads: 861091

Percentage reads mapped: 99.19

Strain: lineage4.1.3

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
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
lineage4.1.3 Euro-American T;X;H None 0.99
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 761139 p.His445Tyr missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4327132 c.341delA frameshift_variant 1.0 ethionamide, ethionamide
gid 4407967 p.Leu79Ser missense_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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 1.0
rpoB 762394 p.Val863Ala missense_variant 0.11
rpoB 762505 p.Phe900Ser missense_variant 0.14
rpoC 762836 c.-534C>G upstream_gene_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833696 p.Leu52Pro missense_variant 0.12
tlyA 1917915 c.-25T>C upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156185 c.-74T>C upstream_gene_variant 0.13
katG 2156559 c.-448C>T upstream_gene_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289613 c.-372T>C upstream_gene_variant 0.11
pncA 2289827 c.-586A>G upstream_gene_variant 0.11
pncA 2290201 c.-960G>A upstream_gene_variant 0.12
eis 2714911 p.Thr141Met missense_variant 0.17
eis 2715249 c.84C>T synonymous_variant 0.12
folC 2747392 c.207C>T synonymous_variant 0.12
ribD 2987074 p.Asp79Gly missense_variant 0.11
ribD 2987307 p.Ala157Pro missense_variant 0.25
Rv2752c 3064657 p.Glu512Val missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087265 p.Leu149Pro missense_variant 0.11
fbiD 3339273 c.156T>G synonymous_variant 0.25
Rv3083 3448731 c.228C>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840921 p.Val167Ala missense_variant 0.11
rpoA 3878482 p.Leu9Pro missense_variant 0.13
panD 4044266 c.16C>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244681 c.1449A>G synonymous_variant 0.17
embA 4244938 p.Lys569Arg missense_variant 0.11
embA 4245231 p.Arg667Trp missense_variant 0.12
aftB 4267722 p.Val372Ala missense_variant 0.12
aftB 4267740 p.Glu366Gly missense_variant 0.15
aftB 4267855 c.982C>A synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0