TB-Profiler result

Run: ERR4818539
Summary

Run ID: ERR4818539

Sample name:

Date: 01-04-2023 15:36:58

Number of reads: 711166

Percentage reads mapped: 99.45

Strain: lineage4.1.2.1

Drug-resistance: Other

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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
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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
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 5597 p.Leu120Val missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7930 p.Ala210Val missense_variant 1.0
gyrA 8629 p.Leu443Pro missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491523 c.745delT frameshift_variant 0.18
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoB 759678 c.-129T>C upstream_gene_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764484 p.Arg372Gln missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766817 p.His1150Asn missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779407 c.421dupG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.38
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169272 c.1341C>A synonymous_variant 0.13
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518274 p.Trp54Arg missense_variant 0.15
ahpC 2726338 p.Val49Gly missense_variant 0.29
folC 2746495 p.His368Gln missense_variant 0.22
thyA 3074660 c.-189C>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640415 c.-128T>C upstream_gene_variant 1.0
embC 4240180 c.318G>A synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245143 c.1911C>A synonymous_variant 0.1
embB 4249330 p.Met939Ile missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0