TB-Profiler result

Run: ERR2864297
Summary

Run ID: ERR2864297

Sample name:

Date: 31-03-2023 23:56:21

Number of reads: 1770648

Percentage reads mapped: 99.71

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
fgd1 491370 c.588C>T synonymous_variant 0.12
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765138 p.Thr590Ile missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304628 c.1698G>A synonymous_variant 0.12
atpE 1460931 c.-114_-113insT upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472731 n.886C>G non_coding_transcript_exon_variant 0.17
fabG1 1673560 c.121_122insG frameshift_variant 0.15
fabG1 1674032 p.Ile198Asn missense_variant 0.11
rpsA 1833354 c.-188G>T upstream_gene_variant 0.29
rpsA 1833599 p.Glu20Lys missense_variant 0.15
rpsA 1833610 c.69C>T synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155306 p.Gly269Val missense_variant 0.14
PPE35 2169164 c.1449G>T synonymous_variant 0.15
PPE35 2169910 p.Asn235His missense_variant 0.12
PPE35 2170401 p.Pro71Gln missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518964 p.Gly284Ser missense_variant 0.11
eis 2714149 p.Pro395Leu missense_variant 0.11
eis 2714912 p.Thr141Ala missense_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339081 c.-37A>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475355 p.Leu450Pro missense_variant 0.11
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
embB 4247523 p.Leu337Arg missense_variant 0.13
aftB 4267817 c.1020G>A synonymous_variant 0.17
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