TB-Profiler result

Run: SRR6046179
Summary

Run ID: SRR6046179

Sample name:

Date: 04-04-2023 12:12:36

Number of reads: 996221

Percentage reads mapped: 90.84

Strain: lineage4.1.3

Drug-resistance: HR-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
lineage4.1.3 Euro-American T;X;H None 1.0
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 0.5
ccsA 620748 c.858T>G synonymous_variant 0.29
rpoB 762765 p.Leu987Met missense_variant 0.11
rpoC 764205 p.Asp279Gly missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778620 p.Ala96Pro missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 1.0
Rv1258c 1407363 c.-23C>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154999 c.1113A>C synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726647 p.Gly152Asp missense_variant 0.1
Rv2752c 3067167 c.-976C>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474847 p.Lys281Glu missense_variant 0.11
clpC1 4039714 p.Tyr331His missense_variant 0.1
embC 4241117 p.Thr419Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Pro missense_variant 0.11
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243860 p.Gly210Ser missense_variant 0.12
embA 4245018 p.Gly596Ser missense_variant 0.12
ethA 4326215 p.Glu420Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0