TB-Profiler result

Run: ERR11049117
Summary

Run ID: ERR11049117

Sample name:

Date: 31-03-2023 11:21:46

Number of reads: 3423949

Percentage reads mapped: 99.68

Strain: lineage4.4.1.1;lineage4.1.2

Drug-resistance: Other

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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 0.47
lineage4.4 Euro-American S;T None 0.57
lineage4.1.2 Euro-American T;H None 0.44
lineage4.4.1 Euro-American (S-type) S;T None 0.54
lineage4.4.1.1 Euro-American S;Orphans None 0.53
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
ethR 4327876 p.Phe110Leu missense_variant 0.5 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.48
mshA 576108 p.Ala254Gly missense_variant 0.14
mshA 576482 p.Val379Leu missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 0.44
rpoC 765150 p.Gly594Glu missense_variant 0.47
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 0.36
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 0.53
PPE35 2168303 c.2310G>T synonymous_variant 0.49
PPE35 2169680 c.933A>C synonymous_variant 0.57
PPE35 2169840 p.Gly258Asp missense_variant 0.42
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2222376 c.789T>G synonymous_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.45
pepQ 2860159 p.Ala87Gly missense_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.28
Rv3083 3448608 c.105G>A synonymous_variant 0.54
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.54
alr 3840263 c.1158C>T synonymous_variant 0.54
rpoA 3878613 c.-106A>C upstream_gene_variant 0.27
rpoA 3878641 c.-134C>G upstream_gene_variant 0.2
embC 4240409 p.Pro183Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.43
embB 4246584 p.Arg24Pro missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0