TB-Profiler result

Run: DRR130065
Summary

Run ID: DRR130065

Sample name:

Date: 31-03-2023 07:03:18

Number of reads: 688051

Percentage reads mapped: 98.84

Strain: lineage4.9;lineage2.2.2

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
lineage2 East-Asian Beijing RD105 0.83
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.82
lineage4.9 Euro-American (H37Rv-like) T1 None 0.14
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.9
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 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.85 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.83 isoniazid, ethionamide
katG 2155969 p.Leu48Gln missense_variant 0.89 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 0.8 pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 0.79 cycloserine
embB 4247429 p.Met306Val missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.94
gyrA 9304 p.Gly668Asp missense_variant 0.88
fgd1 491742 c.960T>C synonymous_variant 0.94
rpoB 759939 p.Pro45Ser missense_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.91
rpoC 764126 p.Thr253Ser missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154_-153insC upstream_gene_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833909 p.Asp123Ala missense_variant 0.77
rpsA 1834177 c.636A>C synonymous_variant 0.74
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.9
PPE35 2167926 p.Leu896Ser missense_variant 0.87
PPE35 2168891 c.1722A>G synonymous_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747325 p.Arg92Ser missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 0.76
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.83
Rv3236c 3612813 p.Thr102Ala missense_variant 0.7
clpC1 4039122 p.Val528Ala missense_variant 0.91
embA 4242643 c.-590C>T upstream_gene_variant 0.88
embA 4243460 c.228C>T synonymous_variant 0.79
aftB 4267647 p.Asp397Gly missense_variant 0.95
whiB6 4338594 c.-73T>G upstream_gene_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407927 p.Glu92Asp missense_variant 0.91