TB-Profiler result

Run: ERR2679307
Summary

Run ID: ERR2679307

Sample name:

Date: 31-03-2023 23:01:41

Number of reads: 553490

Percentage reads mapped: 99.37

Strain: lineage4.6.2.2

Drug-resistance: Other

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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
rpsL 781821 p.Lys88Gln missense_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 620289 c.399A>G synonymous_variant 0.13
ccsA 620500 p.Gly204Ser missense_variant 0.14
ccsA 620524 c.634C>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
mmpR5 779009 p.Val7Ala missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.25
Rv1258c 1406450 c.891C>G synonymous_variant 0.12
Rv1258c 1407014 c.327G>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101997 p.Ala349Val missense_variant 0.13
PPE35 2170412 c.201G>A synonymous_variant 0.17
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714783 p.Gln184Glu missense_variant 0.11
eis 2715481 c.-149G>A upstream_gene_variant 0.12
folC 2746998 p.His201Tyr missense_variant 0.14
pepQ 2859829 p.Gly197Glu missense_variant 0.12
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyX 3067837 p.Glu37Lys missense_variant 0.11
thyX 3067850 c.96A>T synonymous_variant 0.11
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475291 p.Phe429Leu missense_variant 0.22
Rv3236c 3612101 p.Ile339Asn missense_variant 0.13
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
fbiB 3641415 c.-120C>T upstream_gene_variant 0.11
rpoA 3878578 c.-71C>A upstream_gene_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244137 p.Ala302Val missense_variant 0.2
embA 4244582 c.1352delG frameshift_variant 0.25
embA 4245183 c.1951C>T synonymous_variant 0.11
embB 4247022 p.Ala170Glu missense_variant 0.15
aftB 4267195 p.Pro548Thr missense_variant 0.15
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4267605 p.Arg411Pro missense_variant 0.2
aftB 4268017 p.Val274Met missense_variant 0.17
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0