TB-Profiler result

Run: SRR20139569
Summary

Run ID: SRR20139569

Sample name:

Date: 13-03-2023 09:23:20

Number of reads: 1640717

Percentage reads mapped: 99.62

Strain: lineage4.1.2.1

Drug-resistance: RR-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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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 5740 c.501G>C synonymous_variant 1.0
gyrA 6922 c.-380G>T upstream_gene_variant 0.18
gyrB 6927 p.Leu563Trp missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.16
fgd1 490756 c.-27T>G upstream_gene_variant 0.25
fgd1 490780 c.-3C>A upstream_gene_variant 0.15
fgd1 490803 c.21T>G synonymous_variant 0.18
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576710 p.Arg455Gly missense_variant 0.14
mshA 576718 c.1371C>G synonymous_variant 0.17
mshA 576731 p.Asp462Ala missense_variant 0.21
mshA 576739 c.1392A>G synonymous_variant 0.17
mshA 576740 p.Ala465Gly missense_variant 0.16
ccsA 620748 c.858T>G synonymous_variant 0.18
rpoB 759615 c.-192A>C upstream_gene_variant 0.27
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.19
fbiC 1303038 c.108T>G synonymous_variant 0.17
fbiC 1303055 p.Asp42Gly missense_variant 0.21
fbiC 1304159 p.Val410Gly missense_variant 0.27
fbiC 1304166 c.1236A>G synonymous_variant 0.16
fbiC 1304174 p.Val415Gly missense_variant 0.18
Rv1258c 1407055 p.Tyr96Asp missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714549 p.Met262Leu missense_variant 0.16
eis 2714552 p.Ser261Pro missense_variant 0.14
eis 2715468 c.-136C>T upstream_gene_variant 1.0
ahpC 2726338 p.Val50Gly missense_variant 0.22
ahpC 2726344 c.153C>T synonymous_variant 0.17
ahpC 2726350 p.Trp53Leu missense_variant 0.38
thyA 3074608 c.-137A>G upstream_gene_variant 0.17
thyA 3074646 c.-177T>G upstream_gene_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
embC 4240188 p.Val109Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249305 p.Asn931Thr missense_variant 0.24
embB 4249323 p.Ala937Glu missense_variant 0.22
ethA 4326060 p.Lys472* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407983 c.217delG frameshift_variant 1.0