TB-Profiler result

Run: SRR1174312
Summary

Run ID: SRR1174312

Sample name:

Date: 03-04-2023 03:34:16

Number of reads: 1225915

Percentage reads mapped: 97.57

Strain: lineage4.6.1.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.2 Euro-American T2 RD724 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 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.97 ethambutol
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
gyrB 6501 p.Arg421His missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491287 p.Gly169Cys missense_variant 0.12
rpoC 764616 p.Asn416Ser missense_variant 0.48
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472069 n.224G>T non_coding_transcript_exon_variant 0.11
inhA 1674465 c.264C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102062 p.Glu327Asp missense_variant 0.11
PPE35 2169320 p.Leu431Phe missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859354 c.1065C>T synonymous_variant 0.14
Rv3083 3449484 p.Lys327Asn missense_variant 0.15
Rv3083 3449752 p.Gly417Ser missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613298 c.-182G>A upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
ubiA 4269148 p.Val229Ala missense_variant 1.0
ethR 4328183 p.Tyr212Cys missense_variant 1.0
ethA 4328214 c.-741C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0