TB-Profiler result

Run: ERR3148151
Summary

Run ID: ERR3148151

Sample name:

Date: 15-08-2022 11:50:54

Number of reads: 358994

Percentage reads mapped: 99.37

Strain: lineage4.1.1.3

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
lineage4.1.1 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288883 p.Leu120Pro missense_variant 1.0 pyrazinamide
pncA 2289067 p.Ser59Pro missense_variant 0.13 pyrazinamide
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 761079 p.Phe425Leu missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 776668 p.Asp605Tyr missense_variant 0.15
mmpS5 779534 c.-629C>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302884 c.-47T>C upstream_gene_variant 0.11
Rv1258c 1406344 p.Asn333Tyr missense_variant 0.15
Rv1258c 1406794 c.547T>C synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473053 n.1208T>C non_coding_transcript_exon_variant 0.14
rrs 1473062 n.1217T>C non_coding_transcript_exon_variant 0.15
rrs 1473304 n.1459C>T non_coding_transcript_exon_variant 0.12
rrl 1476610 n.2953C>T non_coding_transcript_exon_variant 0.14
rpsA 1833727 c.186G>A synonymous_variant 1.0
PPE35 2169632 c.981C>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289729 c.-488C>T upstream_gene_variant 0.2
kasA 2518147 c.33C>T synonymous_variant 0.3
eis 2714150 p.Pro395Thr missense_variant 0.11
folC 2746685 p.Ala305Val missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612897 p.Gly74Ser missense_variant 0.2
fbiA 3641315 p.Thr258Met missense_variant 0.1
fbiB 3641859 p.Asp109Tyr missense_variant 0.14
fbiB 3641902 p.Val123Ala missense_variant 0.14
alr 3841353 p.Leu23* stop_gained 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244340 p.Ser370Pro missense_variant 0.12
embB 4247042 p.Pro177Ser missense_variant 0.12
embB 4247249 p.Gly246Cys missense_variant 0.14
embB 4247498 p.Pro329Thr missense_variant 0.14
ethA 4326900 p.Pro192Thr missense_variant 1.0
whiB6 4338197 p.His109Asn missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0