TB-Profiler result

Run: ERR8975687
Summary

Run ID: ERR8975687

Sample name:

Date: 02-04-2023 08:58:12

Number of reads: 3152544

Percentage reads mapped: 99.73

Strain: lineage4.3.2.1;lineage2.2.2

Drug-resistance: Pre-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
lineage2 East-Asian Beijing RD105 0.59
lineage4 Euro-American LAM;T;S;X;H None 0.42
lineage4.3 Euro-American (LAM) mainly-LAM None 0.39
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.57
lineage4.3.2 Euro-American (LAM) LAM3 None 0.39
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.57
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.37
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
gyrB 6742 p.Glu501Asp missense_variant 0.73 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.37 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.62 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.42 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.62 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.57 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.57 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 0.65 pyrazinamide, pyrazinamide
pncA 2289073 p.His57Tyr missense_variant 0.41 pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 0.55 cycloserine
embA 4243221 c.-12C>T upstream_gene_variant 0.32 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.56 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 0.6 ethionamide
gid 4407967 p.Leu79Ser missense_variant 0.56 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 5520 p.Pro94Leu missense_variant 0.41
gyrA 7222 c.-80C>T upstream_gene_variant 0.34
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 491742 c.960T>C synonymous_variant 0.54
rpoC 763031 c.-339T>C upstream_gene_variant 0.54
rpoC 764995 c.1626C>G synonymous_variant 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.51
mmpR5 779130 c.144dupC frameshift_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.53
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.35
rpsA 1834177 c.636A>C synonymous_variant 0.48
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.65
PPE35 2167926 p.Leu896Ser missense_variant 0.59
Rv1979c 2221939 p.Arg409Gln missense_variant 0.61
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.44
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.58
rpoA 3878630 c.-123G>C upstream_gene_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 0.46
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.6
aftB 4267647 p.Asp397Gly missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.62
gid 4407927 p.Glu92Asp missense_variant 0.59
gid 4408156 p.Leu16Arg missense_variant 0.42