TB-Profiler result

Run: ERR037486
Summary

Run ID: ERR037486

Sample name:

Date: 31-03-2023 08:33:39

Number of reads: 13341303

Percentage reads mapped: 99.69

Strain: lineage4.3.4.2.1

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
lineage4.3 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
lineage4.3.4.2.1 Euro-American (LAM) 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762714 p.Val970Met missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.38
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.26
atpE 1461019 c.-26C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.19
PPE35 2169866 c.747G>C synonymous_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.22
ribD 2987307 p.Ala157Pro missense_variant 0.16
Rv2752c 3064741 p.Gly484Ala missense_variant 0.29
thyA 3073806 c.666C>G synonymous_variant 0.19
thyA 3073868 p.Thr202Ala missense_variant 1.0
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 0.99
fbiB 3641955 p.Gly141Arg missense_variant 0.21
fbiB 3642772 p.Asp413Ala missense_variant 0.17
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878238 p.Asp90Glu missense_variant 0.19
ddn 3987013 p.Gly57Ala missense_variant 0.24
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.21
clpC1 4039932 p.Gly258Val missense_variant 0.28
embC 4239842 c.-21C>A upstream_gene_variant 0.16
embC 4241539 c.1677T>C synonymous_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.18
embC 4242476 p.Pro872Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.41
embB 4248730 c.2217C>T synonymous_variant 0.99
ubiA 4269529 p.Ala102Gly missense_variant 0.2
ethA 4327229 p.Leu82Pro missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0