TB-Profiler result

Run: ERR245759
Summary

Run ID: ERR245759

Sample name:

Date: 31-03-2023 18:18:58

Number of reads: 11646813

Percentage reads mapped: 97.77

Strain: lineage4.1.2.1

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 781687 p.Lys43Arg missense_variant 0.99 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 0.92 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 7493 c.192C>T synonymous_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8445 p.Arg382Gly missense_variant 0.27
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.99
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762249 p.Leu815Val missense_variant 0.2
rpoC 762836 c.-534C>G upstream_gene_variant 0.29
rpoC 764725 p.Phe452Leu missense_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 0.99
rpoC 767305 p.Tyr1312* stop_gained 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406622 p.Leu240Arg missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167871 c.2742G>C synonymous_variant 0.21
PPE35 2169320 p.Leu431Phe missense_variant 0.14
PPE35 2169356 c.1257C>T synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.22
eis 2715586 c.-254G>C upstream_gene_variant 0.35
pepQ 2859381 c.1038C>G synonymous_variant 0.21
ribD 2987307 p.Ala157Pro missense_variant 0.17
Rv2752c 3064741 p.Gly484Ala missense_variant 0.22
thyA 3073817 p.Gln219Glu missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642734 c.1200G>C synonymous_variant 0.17
clpC1 4039932 p.Gly258Val missense_variant 0.36
embC 4241056 c.1194C>G synonymous_variant 0.26
embC 4242425 p.Arg855Gly missense_variant 0.17
embC 4242476 p.Pro872Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.99
embC 4242822 p.Val987Gly missense_variant 0.29
embC 4242827 p.Leu989Val missense_variant 0.17
embA 4244375 c.1143C>G synonymous_variant 0.23
ubiA 4269529 p.Ala102Gly missense_variant 0.24
ethA 4327346 p.Gly43Val missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0