TB-Profiler result

Run: ERR4828777
Summary

Run ID: ERR4828777

Sample name:

Date: 01-04-2023 19:04:37

Number of reads: 946590

Percentage reads mapped: 99.43

Strain: lineage4.2.1.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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 761110 p.Asp435Val missense_variant 0.16 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288957 p.Tyr95* stop_gained 1.0 pyrazinamide
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol
ethA 4327132 c.341delA frameshift_variant 0.11 ethionamide, ethionamide
ethA 4327409 p.His22Pro missense_variant 1.0 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 8457 p.Glu386Lys missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575833 c.486C>T synonymous_variant 1.0
mshA 576092 p.Pro249Ala missense_variant 1.0
rpoC 764081 p.Glu238Lys missense_variant 0.14
rpoC 764363 p.Gly332Ser missense_variant 0.57
rpoC 764923 p.Glu518Asp missense_variant 0.39
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800973 c.165C>T synonymous_variant 1.0
Rv1258c 1407451 c.-111C>G upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673850 p.Phe137Leu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102759 p.Ala95Val missense_variant 0.1
PPE35 2169879 p.Phe245Cys missense_variant 0.91
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.4
PPE35 2170613 c.-1G>A upstream_gene_variant 1.0
PPE35 2170656 c.-44T>C upstream_gene_variant 0.1
Rv1979c 2222106 p.Phe353Leu missense_variant 0.12
Rv1979c 2222727 c.438C>T synonymous_variant 0.13
Rv1979c 2222755 p.Lys137Arg missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714468 p.Trp289Arg missense_variant 0.1
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449132 p.Leu210Arg missense_variant 0.92
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641134 p.Glu198Lys missense_variant 0.14
ddn 3987092 p.Glu83Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246587 p.Gly25Ala missense_variant 1.0
embB 4247790 p.Ser426Asn missense_variant 0.95
aftB 4268228 c.609C>A synonymous_variant 0.17
aftB 4268869 c.-33C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407969 c.233dupC frameshift_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0