TB-Profiler result

Run: SRR4035899

Summary

Run ID: SRR4035899

Sample name:

Date: 04-04-2023 07:22:07

Number of reads: 520534

Percentage reads mapped: 99.6

Strain: lineage4.3.2.1

Drug-resistance: Sensitive


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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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8191 p.Ala297Val missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619898 p.Thr3Met missense_variant 0.14
rpoC 762836 c.-534C>G upstream_gene_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765433 p.Met688Ile missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775959 p.Ile841Asn missense_variant 0.2
mmpL5 778380 p.Pro34Leu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918740 c.801C>A synonymous_variant 0.25
PPE35 2169320 p.Leu431Phe missense_variant 0.5
PPE35 2170548 p.Gly22Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518702 c.588C>T synonymous_variant 0.14
thyA 3073806 c.666C>G synonymous_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4043891 c.389_390delAG frameshift_variant 0.18
embC 4242106 c.2244C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248820 c.2307C>T synonymous_variant 0.13
aftB 4267086 c.1750delC frameshift_variant 0.2
aftB 4268999 c.-163C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0