TB-Profiler result

Run: ERR038739
Summary

Run ID: ERR038739

Sample name:

Date: 31-03-2023 08:41:40

Number of reads: 25731319

Percentage reads mapped: 99.59

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 1.0
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 2289207 p.Asp12Ala missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
ethA 4327147 p.Trp109* stop_gained 0.99 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 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.26
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.21
inhA 1674465 c.264C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.18
PPE35 2169866 c.747G>C synonymous_variant 0.37
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.21
eis 2715586 c.-254G>C upstream_gene_variant 0.45
ahpC 2726287 p.Gly32Asp missense_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.23
Rv2752c 3064552 p.Arg547Pro missense_variant 0.22
Rv2752c 3064741 p.Gly484Ala missense_variant 0.28
thyA 3073806 c.666C>G synonymous_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613029 c.88T>C synonymous_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.23
fbiB 3642734 c.1200G>C synonymous_variant 0.18
fbiB 3642772 p.Asp413Ala missense_variant 0.17
clpC1 4038857 c.1848C>A synonymous_variant 0.22
clpC1 4039932 p.Gly258Val missense_variant 0.34
embC 4239842 c.-21C>A upstream_gene_variant 0.17
embC 4242425 p.Arg855Gly missense_variant 0.21
embC 4242476 p.Pro872Ala missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.43
embA 4243709 c.477C>T synonymous_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.25
ethA 4327672 c.-199G>A upstream_gene_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4408115 p.Gly30Arg missense_variant 1.0