TB-Profiler result

Run: SRR4033489
Summary

Run ID: SRR4033489

Sample name:

Date: 04-04-2023 06:07:46

Number of reads: 999864

Percentage reads mapped: 99.68

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 0.99
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 2155660 c.451delG frameshift_variant 0.11 isoniazid
pncA 2288730 p.Ala171Val missense_variant 0.12 pyrazinamide
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 8508 p.Glu403Lys missense_variant 0.12
gyrA 9059 c.1758G>A synonymous_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302887 c.-43delG upstream_gene_variant 0.13
fbiC 1304381 p.Ala484Val missense_variant 0.14
fbiC 1305076 p.Pro716Thr missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
inhA 1674082 c.-120G>A upstream_gene_variant 0.1
inhA 1674952 p.Pro251Ala missense_variant 0.18
rpsA 1834675 c.1138_1142delATGGC frameshift_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168473 c.2139delC frameshift_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289019 p.Gly75Ser missense_variant 0.14
Rv2752c 3064656 c.1536G>A synonymous_variant 0.1
thyA 3073806 c.666C>G synonymous_variant 0.22
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
clpC1 4039330 p.Ala459Thr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245943 p.Arg904His missense_variant 0.11
embA 4246221 p.Leu997Phe missense_variant 0.11
aftB 4267851 p.Gln329Leu missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0