TB-Profiler result

Run: ERR245686
Summary

Run ID: ERR245686

Sample name:

Date: 31-03-2023 18:15:08

Number of reads: 14724913

Percentage reads mapped: 99.39

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
ethA 4327054 p.Tyr140* stop_gained 0.17 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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7162 c.-140C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.21
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575932 p.Glu195Asp missense_variant 0.22
rpoB 759620 c.-187A>C upstream_gene_variant 0.36
rpoB 760478 c.672C>T synonymous_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.28
rpoC 764725 p.Phe452Leu missense_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 1.0
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
fbiC 1304242 p.Pro438Ser missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.23
inhA 1674892 p.Asn231Asp missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167871 c.2742G>C synonymous_variant 0.17
PPE35 2169866 c.747G>C synonymous_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.21
eis 2714569 p.Ala255Gly missense_variant 0.23
eis 2715586 c.-254G>C upstream_gene_variant 0.3
ahpC 2725954 c.-239C>T upstream_gene_variant 0.26
folC 2746186 c.1413G>C synonymous_variant 0.2
pepQ 2859974 p.Ala149Pro missense_variant 0.16
Rv2752c 3064741 p.Gly484Ala missense_variant 0.39
thyA 3073817 p.Gln219Glu missense_variant 0.26
thyA 3073868 p.Thr202Ala missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.22
fbiB 3642734 c.1200G>C synonymous_variant 0.16
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039932 p.Gly258Val missense_variant 0.3
embC 4241056 c.1194C>G synonymous_variant 0.28
embC 4242476 p.Pro872Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.27
embA 4244375 c.1143C>G synonymous_variant 0.26
embB 4247041 c.528C>T synonymous_variant 0.18
ubiA 4269529 p.Ala102Gly missense_variant 0.18
ethA 4327672 c.-199G>A upstream_gene_variant 0.25
ethA 4328019 c.-546G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0