TB-Profiler result

Run: ERR046981
Summary

Run ID: ERR046981

Sample name:

Date: 31-03-2023 08:59:43

Number of reads: 5790998

Percentage reads mapped: 99.78

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 0.99
mmpR5 779371 p.Ala128Pro missense_variant 0.24
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.22
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.36
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.24
folC 2747263 c.336C>A synonymous_variant 0.15
pepQ 2859381 c.1038C>G synonymous_variant 0.16
Rv2752c 3064552 p.Arg547Pro missense_variant 0.19
Rv2752c 3064741 p.Gly484Ala missense_variant 0.24
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.15
fbiD 3339273 c.156T>G synonymous_variant 0.36
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
fbiB 3642734 c.1200G>C synonymous_variant 0.21
fbiB 3642772 p.Asp413Ala missense_variant 0.27
rpoA 3878238 p.Asp90Glu missense_variant 0.21
clpC1 4038857 c.1848C>A synonymous_variant 0.24
clpC1 4039932 p.Gly258Val missense_variant 0.29
embC 4239842 c.-21C>A upstream_gene_variant 0.17
embC 4241456 p.Ala532Pro missense_variant 0.4
embC 4242476 p.Pro872Ala missense_variant 0.21
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.28
aftB 4267272 p.Lys522Arg missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.15
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.23
ethA 4328004 c.-531C>T upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0