TB-Profiler result

Run: ERR9811807
Summary

Run ID: ERR9811807

Sample name:

Date: 02-04-2023 13:14:39

Number of reads: 1062620

Percentage reads mapped: 99.74

Strain: lineage4.3.4.2

Drug-resistance: Pre-XDR-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
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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2288868 p.Val125Gly missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4247781 p.Met423Thr missense_variant 1.0 ethambutol
gid 4407965 p.Ala80Pro missense_variant 1.0 streptomycin
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
fgd1 490655 c.-128T>C upstream_gene_variant 1.0
mshA 576483 p.Val379Gly missense_variant 0.27
mshA 576616 c.1269G>C synonymous_variant 0.33
mshA 576693 p.Asn449Thr missense_variant 0.25
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918621 p.Ser228Arg missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289787 c.-546A>C upstream_gene_variant 0.2
thyX 3067958 c.-13T>G upstream_gene_variant 0.19
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339044 c.-74T>G upstream_gene_variant 0.26
fbiD 3339734 p.Ala206Gly missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474212 p.Lys69Thr missense_variant 0.19
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3841433 c.-13G>C upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.33
embB 4247033 p.Ser174Arg missense_variant 0.22
embB 4248328 c.1815G>C synonymous_variant 0.12
aftB 4267418 c.1419G>A synonymous_variant 0.1
aftB 4267902 p.Val312Gly missense_variant 0.18
aftB 4268619 p.Val73Gly missense_variant 0.33
ethR 4328041 p.Thr165Pro missense_variant 0.19
ethA 4328127 c.-654C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0