TB-Profiler result

Run: SRR4035872
Summary

Run ID: SRR4035872

Sample name:

Date: 04-04-2023 07:21:14

Number of reads: 1202165

Percentage reads mapped: 99.62

Strain: lineage4.3.2.1

Drug-resistance: HR-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
lineage4.3 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
katG 2154075 c.2029_2036delACCTACCA frameshift_variant 0.11 isoniazid
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 9304 p.Gly668Asp missense_variant 1.0
mshA 576287 c.940C>A synonymous_variant 0.13
ccsA 620661 c.771C>T synonymous_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766488 p.Pro1040Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777010 p.Pro491Ser 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
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918187 p.Gly83Asp missense_variant 0.18
katG 2154712 p.Leu467Ser missense_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518792 c.678C>T synonymous_variant 0.11
folC 2746376 p.Ser408* stop_gained 0.11
folC 2747359 c.240C>A synonymous_variant 0.11
ribD 2986946 c.108T>C synonymous_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448830 p.Trp109Cys missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.15
fbiB 3641990 p.Met152Ile missense_variant 0.15
fbiB 3642636 p.Ala368Thr missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241619 p.Trp586* stop_gained 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243396 p.Ile55Thr missense_variant 0.13
embB 4247916 p.Arg468His missense_variant 0.15
embB 4249398 p.Ala962Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407743 p.Arg154Trp missense_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408448 c.-246A>G upstream_gene_variant 0.11