TB-Profiler result

Run: ERR11044606
Summary

Run ID: ERR11044606

Sample name:

Date: 31-03-2023 11:56:42

Number of reads: 5168872

Percentage reads mapped: 99.65

Strain: lineage4.6.2.2

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
lineage4.6 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
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 6358 c.-944C>T upstream_gene_variant 1.0
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 0.13
rpoB 762715 p.Val970Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_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
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289102 p.Thr47Ile missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.18
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyA 3073859 p.Asp205Tyr missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.47
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3449073 c.570C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878613 c.-106A>C upstream_gene_variant 0.37
rpoA 3878641 c.-134C>G upstream_gene_variant 0.28
embC 4240409 p.Pro183Ala missense_variant 0.2
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245227 c.1995C>T synonymous_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.16
embB 4248324 p.Ala604Gly missense_variant 0.26
aftB 4267272 p.Lys522Arg missense_variant 1.0
ubiA 4269319 p.Leu172Gln missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338473 c.49A>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0