TB-Profiler result

Run: ERR10748463
Summary

Run ID: ERR10748463

Sample name:

Date: 31-03-2023 10:55:36

Number of reads: 3447193

Percentage reads mapped: 99.67

Strain: lineage4.7;lineage4.1.1.1

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 0.2
lineage4.7 Euro-American (mainly T) T1;T5 None 0.82
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.2
lineage4.1.1.1 Euro-American (X-type) X2 RD183 0.2
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 0.79 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.83 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.79 isoniazid, ethionamide
katG 2155167 p.Ser315Thr missense_variant 0.78 isoniazid
pncA 2288952 p.Gly97Asp missense_variant 0.76 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.75 ethambutol
ethA 4326449 p.Thr342Lys missense_variant 0.89 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 0.27
gyrA 9304 p.Gly668Asp missense_variant 0.25
rpoC 764817 p.Val483Gly missense_variant 0.83
rpoC 765150 p.Gly594Glu missense_variant 0.2
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
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.63
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 0.16
fbiD 3339734 p.Ala206Gly missense_variant 0.64
fbiD 3339746 p.Ala210Gly missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.19
fbiA 3641447 p.Thr302Met missense_variant 0.15
rpoA 3877553 p.Glu319Lys missense_variant 0.2
rpoA 3878641 c.-134C>G upstream_gene_variant 0.27
embC 4240897 c.1035C>G synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.15
embB 4248324 p.Ala604Gly missense_variant 0.25
embB 4249408 c.2895G>A synonymous_variant 0.23
embB 4249732 c.3219C>G synonymous_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407704 p.Ala167Pro missense_variant 0.8