TB-Profiler result

Run: SRR023478

Summary

Run ID: SRR023478

Sample name:

Date: 02-04-2023 14:12:54

Number of reads: 9955113

Percentage reads mapped: 81.68

Strain: lineage4.1.1.3

Drug-resistance: MDR-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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin
katG 2154730 p.Gln461Pro missense_variant 1.0 isoniazid
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
ccsA 619831 c.-60T>G upstream_gene_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777299 c.1182G>C synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801247 p.Arg147Ser missense_variant 0.14
fbiC 1304077 p.Glu383Lys missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155343 p.Met257Val missense_variant 1.0
PPE35 2170438 p.Gly59Cys missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289017 c.225T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841124 c.297G>T synonymous_variant 0.17
rpoA 3877952 p.Arg186Cys missense_variant 0.98
rpoA 3878641 c.-135delG upstream_gene_variant 0.12
panD 4044480 c.-199G>A upstream_gene_variant 0.22
embC 4242446 p.Ala862Ser missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248658 c.2145G>T synonymous_variant 0.33
embB 4249408 c.2895G>A synonymous_variant 1.0
ethR 4327997 p.Ala150Asp missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0