TB-Profiler result

Run: ERR4800290

Summary

Run ID: ERR4800290

Sample name:

Date: 16-08-2022 08:56:18

Number of reads: 2854301

Percentage reads mapped: 99.58

Strain: lineage4.8;lineage2.2.1.1

Drug-resistance: 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
lineage2 East-Asian Beijing RD105 0.24
lineage4 Euro-American LAM;T;S;X;H None 0.79
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.2
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.76
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.2
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.22
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 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 0.17 rifampicin
rpoB 761115 p.Asn437Asp missense_variant 0.15 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.16 linezolid
fabG1 1673425 c.-15C>T upstream_gene_variant 0.18 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.26 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 0.23 pyrazinamide
folC 2747151 p.Ser150Gly missense_variant 0.19 para-aminosalicylic_acid
embB 4247393 p.Gly294Ser missense_variant 0.2 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 0.24 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.21
gyrA 9304 p.Gly668Asp missense_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 0.27
mshA 575907 p.Ala187Val missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.29
mmpL5 776182 p.Asp767Asn missense_variant 0.26
mmpS5 779615 c.-710C>G upstream_gene_variant 0.28
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.87
rpsA 1834177 c.636A>C synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.23
katG 2156354 c.-243G>A upstream_gene_variant 0.19
PPE35 2167926 p.Leu896Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289045 p.Ser66Leu missense_variant 0.73
eis 2714846 p.Val163Ile missense_variant 0.25
Rv2752c 3065636 p.Pro186Ser missense_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.26
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 0.15
embA 4243460 c.228C>T synonymous_variant 0.16
embB 4247880 p.Val456Ala missense_variant 0.17
embB 4248115 c.1602C>T synonymous_variant 0.3
aftB 4267647 p.Asp397Gly missense_variant 0.2
ethA 4326579 p.Gly299Ser missense_variant 0.76
whiB6 4338254 p.Phe90Leu missense_variant 0.83
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 0.15
gid 4407588 c.615A>G synonymous_variant 0.26
gid 4407927 p.Glu92Asp missense_variant 0.18