TB-Profiler result

Run: SRR832981
Summary

Run ID: SRR832981

Sample name:

Date: 04-04-2023 20:53:18

Number of reads: 5118142

Percentage reads mapped: 98.99

Strain: lineage4.1.2.1

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
lineage4.1 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
gyrA 7582 p.Asp94Gly missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
ald 3086951 c.133delA frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol
gid 4407802 p.Ala134Glu missense_variant 1.0 streptomycin
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 0.95
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575760 p.Arg138His missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406813 c.528T>C synonymous_variant 1.0
Rv1258c 1407170 c.168_170dupGTT disruptive_inframe_insertion 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rpsA 1834884 c.1348_1350dupTCG conservative_inframe_insertion 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714846 c.484_486dupAGC conservative_inframe_insertion 0.21
thyX 3067355 c.591A>G synonymous_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339263 p.Ala49Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840259 p.Tyr388Asp missense_variant 1.0
rpoA 3878634 c.-128_-127insGCC upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247738 p.Ala409Pro missense_variant 1.0
ethA 4326842 p.Tyr211Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0