TB-Profiler result

Run: SRR13068989
Summary

Run ID: SRR13068989

Sample name:

Date: 03-04-2023 08:12:22

Number of reads: 45648

Percentage reads mapped: 99.23

Strain: lineage4.9;lineage2

Drug-resistance: RR-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
lineage2 East-Asian Beijing RD105 0.05
lineage4 Euro-American LAM;T;S;X;H None 0.98
lineage4.9 Euro-American (H37Rv-like) T1 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
pncA 2288823 p.Arg140Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326770 c.703delT frameshift_variant 1.0 ethionamide, 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
mshA 575182 c.-166A>T upstream_gene_variant 0.5
ccsA 620625 p.Ile245Met missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475798 n.2141G>C non_coding_transcript_exon_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448717 p.Val72Met missense_variant 1.0
clpC1 4039565 c.1140G>A synonymous_variant 1.0
clpC1 4039730 c.975C>G synonymous_variant 1.0
clpC1 4040395 p.Gly104Arg missense_variant 0.4
clpC1 4040589 p.His39Arg missense_variant 0.5
embA 4243346 c.114A>G synonymous_variant 1.0
embB 4247647 c.1134G>A synonymous_variant 1.0
embB 4248235 c.1722G>A synonymous_variant 0.4
ethR 4327969 p.Phe141Val missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0