TB-Profiler result

Run: SRR22536487
Summary

Run ID: SRR22536487

Sample name:

Date: 04-04-2023 04:19:38

Number of reads: 1342487

Percentage reads mapped: 99.78

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.81 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288997 p.His82Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326251 c.1222delT frameshift_variant 1.0 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576102 p.Arg252Leu missense_variant 0.14
rpoB 761120 c.1314C>T synonymous_variant 1.0
rpoB 761539 p.Arg578His 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 1304565 c.1635C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473225 n.1380G>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153916 p.Met732Ile missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339736 p.Thr207Pro missense_variant 0.19
Rv3083 3449509 p.Glu336* stop_gained 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245945 p.Ile905Val missense_variant 1.0
embB 4246564 p.Leu17Phe missense_variant 0.14
embB 4246574 p.Ala21Ser missense_variant 0.15
embB 4246582 c.69T>G synonymous_variant 0.15
embB 4247046 p.Asp178Ala missense_variant 0.12
embB 4247055 p.Leu181Gln missense_variant 0.15
embB 4247080 p.Phe189Leu missense_variant 0.13
aftB 4268619 p.Val73Gly missense_variant 0.13
whiB6 4338712 c.-191T>C upstream_gene_variant 1.0
gid 4407833 p.Val124Met missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
whiB6 4338486 c.-192_35del frameshift_variant&start_lost 1.0