TB-Profiler result

Run: ERR038754
Summary

Run ID: ERR038754

Sample name:

Date: 31-03-2023 08:41:51

Number of reads: 20100826

Percentage reads mapped: 99.67

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
rpoC 762836 c.-534C>G upstream_gene_variant 0.36
rpoC 767123 p.Val1252Leu missense_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.18
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.2
eis 2715586 c.-254G>C upstream_gene_variant 0.35
folC 2746923 p.Gly226Ser missense_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.25
Rv2752c 3064552 p.Arg547Pro missense_variant 0.27
thyA 3073806 c.666C>G synonymous_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642734 c.1200G>C synonymous_variant 0.21
fbiB 3642772 p.Asp413Ala missense_variant 0.21
clpC1 4038857 c.1848C>A synonymous_variant 0.24
clpC1 4039932 p.Gly258Val missense_variant 0.25
embC 4242425 p.Arg855Gly missense_variant 0.2
embC 4242476 p.Pro872Ala missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.38
embA 4243692 p.Gly154Ser missense_variant 1.0
embB 4246904 p.Val131Met missense_variant 1.0
ubiA 4269298 p.Ile179Thr missense_variant 0.98
ubiA 4269529 p.Ala102Gly missense_variant 0.22
ethA 4327672 c.-199G>A upstream_gene_variant 0.3
ethA 4328252 c.-779T>G upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407758 p.Ser149Arg missense_variant 1.0