TB-Profiler result

Run: SRR7516376
Summary

Run ID: SRR7516376

Sample name:

Date: 04-04-2023 19:26:32

Number of reads: 1786400

Percentage reads mapped: 99.56

Strain: lineage4.8;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.36
lineage4 Euro-American LAM;T;S;X;H None 0.63
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.39
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.6
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
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.Asp94Gly missense_variant 0.35 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.76 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.31 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.35 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.31 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289030 p.His71Arg missense_variant 0.37 pyrazinamide
pncA 2289089 p.His51Gln missense_variant 0.57 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.43 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.59 ethambutol
embB 4247513 p.Tyr334His missense_variant 0.4 ethambutol
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 6518 p.Val427Met missense_variant 0.51
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 0.26
fgd1 491742 c.960T>C synonymous_variant 0.28
mshA 575907 p.Ala187Val missense_variant 0.34
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.43
rpoC 764817 p.Val483Gly missense_variant 0.31
rpoC 766645 p.Glu1092Asp missense_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.42
mmpL5 776182 p.Asp767Asn missense_variant 0.39
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.3
embR 1416476 p.Tyr291Cys missense_variant 0.68
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.71
rpsA 1834177 c.636A>C synonymous_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.39
PPE35 2167926 p.Leu896Ser missense_variant 0.52
PPE35 2168149 p.Pro822Ser missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518912 c.798G>C synonymous_variant 0.7
ald 3086788 c.-32T>C upstream_gene_variant 0.26
ald 3087532 p.Ala238Asp missense_variant 0.42
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.43
Rv3236c 3612229 c.888C>T synonymous_variant 0.28
Rv3236c 3612813 p.Thr102Ala missense_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.43
gid 4407927 p.Glu92Asp missense_variant 0.33