TB-Profiler result

Run: SRR1174313
Summary

Run ID: SRR1174313

Sample name:

Date: 03-04-2023 03:34:18

Number of reads: 1127416

Percentage reads mapped: 93.73

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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288926 c.306_315delGTACAGCGGC frameshift_variant 0.14 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 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
gyrB 7166 p.Ala643Thr missense_variant 0.12
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 9276 c.1975C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762640 p.Gly945Val missense_variant 0.11
rpoC 764724 p.Phe452Cys missense_variant 1.0
rpoC 764810 p.Pro481Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303391 p.Arg154His missense_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918396 p.Ala153Ser missense_variant 0.14
katG 2155142 p.Thr324Ala missense_variant 0.35
katG 2155541 p.Trp191Gly missense_variant 1.0
PPE35 2169101 c.1512G>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288754 p.Val163Ala missense_variant 1.0
ahpC 2725967 c.-226G>T upstream_gene_variant 0.12
folC 2746723 c.876G>A synonymous_variant 0.11
folC 2746903 c.696G>A synonymous_variant 0.14
folC 2746928 p.Pro224His missense_variant 0.13
Rv2752c 3065920 p.Pro91Leu missense_variant 1.0
thyX 3067404 p.Thr181Ile missense_variant 0.12
thyA 3074663 c.-192T>A upstream_gene_variant 0.13
ald 3087316 p.Val166Ala missense_variant 0.11
ald 3087320 p.Glu167Asp missense_variant 0.11
ald 3087325 c.508_509insGTTCG frameshift_variant 0.11
Rv3083 3449097 c.594C>A synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640407 c.-136G>A upstream_gene_variant 1.0
fbiB 3641637 p.Ala35Ser missense_variant 0.15
ddn 3987172 p.Thr110Asn missense_variant 0.12
clpC1 4039042 p.Ser555Pro missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243239 p.His3Asn missense_variant 0.15
embA 4244931 p.Pro567Thr missense_variant 0.11
embA 4245055 p.Thr608Asn missense_variant 1.0
ubiA 4269731 p.Ala35Thr missense_variant 0.94
ethA 4327107 p.His123Tyr missense_variant 1.0
ethR 4328171 p.Val208Ala missense_variant 1.0
whiB6 4338445 c.76delC frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0