TB-Profiler result

Run: ERR2516698
Summary

Run ID: ERR2516698

Sample name:

Date: 31-03-2023 21:41:15

Number of reads: 3835781

Percentage reads mapped: 99.62

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 7570 p.Ala90Val missense_variant 0.67 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289202 p.Cys14Gly missense_variant 1.0 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4326082 c.1391dupA frameshift_variant 0.58 ethionamide, ethionamide
gid 4408087 c.115delC frameshift_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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620280 c.390C>T synonymous_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761292 p.Val496Met missense_variant 0.31
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766487 p.Pro1040Ser missense_variant 0.58
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 2715432 c.-100C>T upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.16
thyA 3074449 p.Leu8Gln 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 4038857 c.1848C>A synonymous_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.99
embA 4243225 c.-8C>T upstream_gene_variant 0.99
embB 4249773 p.Gly1087Asp missense_variant 0.73
ethA 4327145 p.Ser110Trp missense_variant 1.0
ethA 4327322 p.Pro51His missense_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0