TB-Profiler result

Run: SRR6207292
Summary

Run ID: SRR6207292

Sample name:

Date: 02-08-2023 15:16:24

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490748 c.-35G>T upstream_gene_variant 0.1
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760839 p.Gly345Ser missense_variant 0.12
rpoB 762664 p.Leu953Pro missense_variant 0.11
rpoC 763790 p.Glu141Lys missense_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407165 p.Thr59Met missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475848 n.2191A>G non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918357 p.Thr140Ala missense_variant 0.13
PPE35 2167943 c.2670G>A synonymous_variant 0.12
PPE35 2169746 c.867T>C synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518278 p.Asp55Gly missense_variant 0.12
kasA 2518524 p.Val137Ala missense_variant 0.13
eis 2715432 c.-100C>T upstream_gene_variant 0.18
eis 2715436 c.-104G>A upstream_gene_variant 0.17
eis 2715440 c.-108A>C upstream_gene_variant 0.17
eis 2715445 c.-113C>T upstream_gene_variant 0.17
eis 2715447 c.-115T>A upstream_gene_variant 0.17
eis 2715450 c.-118T>C upstream_gene_variant 0.17
eis 2715451 c.-119C>A upstream_gene_variant 0.17
eis 2715454 c.-122T>G upstream_gene_variant 0.17
eis 2715455 c.-123G>A upstream_gene_variant 0.17
eis 2715458 c.-126T>A upstream_gene_variant 0.17
eis 2715460 c.-128A>G upstream_gene_variant 0.17
eis 2715465 c.-133G>T upstream_gene_variant 0.17
eis 2715469 c.-137T>C upstream_gene_variant 0.15
eis 2715473 c.-141A>G upstream_gene_variant 0.15
ahpC 2726261 c.69G>A synonymous_variant 0.12
folC 2747112 p.Phe163Leu missense_variant 0.15
ribD 2986897 p.Val20Ala missense_variant 0.1
Rv2752c 3066204 c.-13G>T upstream_gene_variant 0.15
thyX 3067591 p.Pro119Ser missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087009 p.Val64Leu missense_variant 0.11
ald 3087161 c.342A>G synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3613309 c.-193G>A upstream_gene_variant 0.14
alr 3840226 p.Thr399Pro missense_variant 0.15
alr 3841444 c.-24G>A upstream_gene_variant 0.13
clpC1 4039484 c.1221T>G synonymous_variant 0.18
clpC1 4039492 p.Glu405Lys missense_variant 0.11
panD 4044313 c.-32C>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242824 p.Gly988Trp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408424 c.-222C>A upstream_gene_variant 0.15