TB-Profiler result

Run: ERR1679645

Summary

Run ID: ERR1679645

Sample name:

Date: 31-03-2023 14:55:25

Number of reads: 748098

Percentage reads mapped: 99.67

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
gid 4407796 p.Ser136* stop_gained 0.11 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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776031 p.Gly817Glu missense_variant 0.1
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
mmpL5 778678 c.-198C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407375 c.-36delC upstream_gene_variant 0.18
Rv1258c 1407524 c.-184A>T upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476306 n.2649A>G non_coding_transcript_exon_variant 0.1
inhA 1674823 p.Gly208Ser missense_variant 0.1
rpsA 1834869 p.Arg443His missense_variant 0.11
rpsA 1834908 p.Ser456Leu missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102204 c.838dupG frameshift_variant 0.18
katG 2155541 p.Trp191Gly missense_variant 1.0
PPE35 2169509 c.1104T>C synonymous_variant 0.1
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518226 p.Ala38Thr missense_variant 0.1
kasA 2518619 p.Ser169Thr missense_variant 0.18
eis 2715344 c.-12C>A upstream_gene_variant 0.1
thyX 3067474 p.Pro158Ala missense_variant 1.0
ald 3087034 c.216delC frameshift_variant 0.12
ald 3087494 c.675C>G synonymous_variant 0.11
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
fbiB 3641555 c.21C>T synonymous_variant 0.14
alr 3840966 p.Ala152Val missense_variant 0.1
alr 3841594 c.-174T>C upstream_gene_variant 1.0
rpoA 3878658 c.-151A>G upstream_gene_variant 0.25
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243724 c.492G>A synonymous_variant 0.11
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4327560 c.-87G>T upstream_gene_variant 0.1
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407980 p.Pro75Ser missense_variant 1.0