TB-Profiler result

Run: SRR21276937
Summary

Run ID: SRR21276937

Sample name:

Date: 04-04-2023 00:14:46

Number of reads: 8178675

Percentage reads mapped: 99.27

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 0.99
lineage4.4 Euro-American S;T None 0.98
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 761100 c.1296_1304delATTCATGGA disruptive_inframe_deletion 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2283387 c.-1787_*5293del transcript_ablation 1.0 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 575907 p.Ala187Val missense_variant 0.12
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
pncA 2289598 c.-357T>C upstream_gene_variant 0.33
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-135delG upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243119 p.Trp1086* stop_gained 0.99
embC 4243146 c.3284A>G stop_lost&splice_region_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.99
embB 4247249 p.Gly246Arg missense_variant 0.95
aftB 4268918 c.-82G>T upstream_gene_variant 0.97
aftB 4268928 c.-92C>T upstream_gene_variant 0.97
aftB 4269375 c.-539G>A upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407898 p.Arg102Pro missense_variant 1.0