TB-Profiler result

Run: ERR4972534
Summary

Run ID: ERR4972534

Sample name:

Date: 01-04-2023 21:45:51

Number of reads: 4427408

Percentage reads mapped: 99.71

Strain: lineage4.4.1.1;lineage4.3.3

Drug-resistance: XDR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.56
lineage4.4 Euro-American S;T None 0.42
lineage4.4.1 Euro-American (S-type) S;T None 0.47
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.56
lineage4.4.1.1 Euro-American S;Orphans None 0.45
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 7570 p.Ala90Val missense_variant 0.58 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.37 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.6 rifampicin
rplC 801268 p.Cys154Arg missense_variant 0.57 linezolid
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.64 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288927 c.314dupG frameshift_variant 0.61 pyrazinamide, pyrazinamide
pncA 2289216 p.Val9Ala missense_variant 0.38 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
ethA 4326802 c.671delA frameshift_variant 0.46 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 6825 p.Leu529Pro missense_variant 0.6
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7677 p.Ala126Pro missense_variant 0.41
gyrA 8040 p.Gly247Ser missense_variant 0.56
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.19
mshA 576482 p.Val379Leu missense_variant 0.11
ccsA 620290 p.Tyr134His missense_variant 0.51
rpoC 764918 p.Val517Leu missense_variant 0.56
rpoC 764995 c.1626C>G synonymous_variant 0.52
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
rrs 1473106 n.1261A>G non_coding_transcript_exon_variant 0.4
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.59
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.32
PPE35 2167870 p.Gly915* stop_gained 0.55
PPE35 2169840 p.Gly258Asp missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.57
folC 2746603 c.996C>T synonymous_variant 0.38
thyA 3073868 p.Thr202Ala missense_variant 0.55
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.21
Rv3083 3448608 c.105G>A synonymous_variant 0.46
Rv3083 3449854 p.Met451Val missense_variant 0.61
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.41
clpC1 4038287 c.2418C>T synonymous_variant 0.54
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.24
ethA 4327416 p.Ala20Thr missense_variant 0.37
whiB6 4338594 c.-73T>A upstream_gene_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407854 p.Gly117Arg missense_variant 0.43
gid 4408096 p.Val36Ala missense_variant 0.55
gid 4408156 p.Leu16Arg missense_variant 0.56
gid 4408233 c.-31A>G upstream_gene_variant 0.56