TB-Profiler result

Run: SRR21276969
Summary

Run ID: SRR21276969

Sample name:

Date: 04-04-2023 00:18:46

Number of reads: 10094052

Percentage reads mapped: 98.54

Strain: lineage4.4.2

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.2 Euro-American T1;T2 None 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 761139 p.His445Cys missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289202 p.Cys14Gly missense_variant 0.99 pyrazinamide
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 576108 p.Ala254Gly missense_variant 0.27
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
Rv2752c 3066099 p.Met31Ile missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
panD 4043882 p.Pro134Ala missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.27
embB 4247829 p.Ala439Val missense_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 0.99
aftB 4269375 c.-539G>A upstream_gene_variant 0.99
ethA 4327190 p.Asp95Gly missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407781 p.Ala141Gly missense_variant 0.58
gid 4408066 p.Asp46Val missense_variant 0.4
gid 4407779 c.136_423del conservative_inframe_deletion 1.0