TB-Profiler result

Run: ERR2653186
Summary

Run ID: ERR2653186

Sample name:

Date: 31-03-2023 22:38:42

Number of reads: 7644979

Percentage reads mapped: 97.47

Strain: lineage4.3.4.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.99
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 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760663 p.Ala286Val missense_variant 1.0 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288717 p.Met175Ile missense_variant 0.99 pyrazinamide
folC 2747151 p.Ser150Gly missense_variant 0.99 para-aminosalicylic_acid
embB 4247730 p.Gly406Ala missense_variant 0.99 ethambutol
gid 4408100 c.102delG frameshift_variant 0.99 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576171 p.Gln275Pro missense_variant 0.97
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779351 p.Gly121Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473334 n.1489C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2222854 p.Ile104Thr missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
ald 3087576 c.759_760dupAC frameshift_variant 0.95
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
Rv3236c 3612009 p.Ala370Thr missense_variant 0.99
alr 3841147 p.Ala92Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0