TB-Profiler result

Run: ERR4796975
Summary

Run ID: ERR4796975

Sample name:

Date: 01-04-2023 07:15:14

Number of reads: 5074971

Percentage reads mapped: 99.74

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
gid 4408100 c.102delG 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 9304 p.Gly668Asp missense_variant 1.0
rpoB 762167 c.2361T>C synonymous_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 1.0
mmpL5 775639 p.Ile948Val 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
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154345 c.1767C>A synonymous_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.71
fbiD 3339744 c.627A>C synonymous_variant 0.33
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.21
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3878590 c.-84_-83insC upstream_gene_variant 1.0
rpoA 3878637 c.-130G>C upstream_gene_variant 0.21
rpoA 3878641 c.-134C>G upstream_gene_variant 0.33
embC 4240409 p.Pro183Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243854 p.Leu208Phe missense_variant 0.99
embB 4246584 p.Arg24Pro missense_variant 0.29
aftB 4267925 c.912G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0