TB-Profiler result

Run: ERR040135
Summary

Run ID: ERR040135

Sample name:

Date: 31-03-2023 08:47:00

Number of reads: 17351451

Percentage reads mapped: 99.25

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 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.99 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
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
rpoC 762836 c.-534C>G upstream_gene_variant 0.3
rpoC 764810 p.Pro481Thr missense_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303391 p.Arg154His missense_variant 1.0
Rv1258c 1407522 c.-182C>G upstream_gene_variant 0.29
embR 1416410 p.Leu313Arg missense_variant 0.99
atpE 1461019 c.-26C>A upstream_gene_variant 0.26
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.18
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.2
PPE35 2169866 c.747G>C synonymous_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.23
pepQ 2859381 c.1038C>G synonymous_variant 0.26
Rv2752c 3064552 p.Arg547Pro missense_variant 0.23
Rv2752c 3064741 p.Gly484Ala missense_variant 0.25
Rv2752c 3065920 p.Pro91Leu missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.26
fbiB 3642734 c.1200G>C synonymous_variant 0.24
rpoA 3878238 p.Asp90Glu missense_variant 0.15
clpC1 4039932 p.Gly258Val missense_variant 0.35
embC 4242425 p.Arg855Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.47
embC 4242827 p.Leu989Val missense_variant 0.23
embA 4244375 c.1143C>G synonymous_variant 0.27
embA 4245055 p.Thr608Asn missense_variant 0.99
ubiA 4269131 p.Leu235Val missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.24
ethA 4327107 p.His123Tyr missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.26
ethR 4328171 p.Val208Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0