TB-Profiler result

Run: ERR6358962
Summary

Run ID: ERR6358962

Sample name:

Date: 02-04-2023 02:26:12

Number of reads: 978083

Percentage reads mapped: 99.69

Strain: lineage4.6.1.2

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 0.99
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.2 Euro-American T2 RD724 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 1.0 pyrazinamide
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol
ethA 4326249 c.1215_1224delGTTGAATTAC 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
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8816 c.1515C>A synonymous_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575961 p.Gln205Leu missense_variant 0.17
rpoC 764810 p.Pro481Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.6
embR 1416410 p.Leu313Arg missense_variant 0.91
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834736 p.Glu399Lys missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170692 c.-80T>G upstream_gene_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714308 p.Pro342Leu missense_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.25
Rv2752c 3065920 p.Pro91Leu missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877967 p.Thr181Ala missense_variant 1.0
panD 4044479 c.-198C>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
aftB 4267834 c.997_1002delTTTATG conservative_inframe_deletion 0.13
aftB 4267843 p.Asp332His missense_variant 0.13
aftB 4267864 p.Tyr325Asn missense_variant 0.12
aftB 4267867 p.Leu324Met missense_variant 0.14
aftB 4267870 p.Ala323Thr missense_variant 0.13
aftB 4267872 p.Gln322Pro missense_variant 0.13
aftB 4267876 c.959_960delTG frameshift_variant 0.13
aftB 4267881 p.Gly319Ala missense_variant 0.13
aftB 4267882 c.954_955insAC frameshift_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 1.0