TB-Profiler result

Run: ERR4796733
Summary

Run ID: ERR4796733

Sample name:

Date: 01-04-2023 07:04:09

Number of reads: 2757040

Percentage reads mapped: 99.62

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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289216 p.Val9Gly missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
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
mshA 576108 p.Ala254Gly missense_variant 0.34
mshA 576482 p.Val379Leu missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767123 p.Val1252Leu missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775960 p.Ile841Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747195 p.Asp135Val missense_variant 0.77
thyA 3074468 p.Thr2Pro missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086982 p.Ala55Pro missense_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
ald 3087015 p.Ala66Pro missense_variant 0.47
ald 3087040 p.Val74Ala missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246542 p.Ser10Asn missense_variant 0.26
embB 4246584 p.Arg24Pro missense_variant 0.47
embB 4249408 c.2895G>A synonymous_variant 0.99
ethA 4327368 p.Glu36Lys missense_variant 1.0
ethA 4328276 c.-805_-804delAT upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407760 c.442dupT frameshift_variant 0.99