TB-Profiler result

Run: DRR130141
Summary

Run ID: DRR130141

Sample name:

Date: 31-03-2023 07:06:16

Number of reads: 1320017

Percentage reads mapped: 99.24

Strain: lineage2.1

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 1.0
lineage2.1 East-Asian (non-Beijing) None None 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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761151 p.Leu449Met missense_variant 0.87 rifampicin
rpoB 761155 p.Ser450Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.96 isoniazid, ethionamide
tlyA 1918597 c.660delG frameshift_variant 0.95 capreomycin
eis 2715342 c.-10G>A upstream_gene_variant 0.76 kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 0.97 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326419 c.1054delG frameshift_variant 0.92 ethionamide, 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765121 c.1752G>A synonymous_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778706 p.Val67Gly missense_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302789 c.-142C>T upstream_gene_variant 0.92
fbiC 1303882 p.Val318Ile missense_variant 0.12
fbiC 1304443 p.Ala505Thr missense_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155607 p.Gly169Ser missense_variant 0.89
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074061 c.339_410delCGCGGCGCTGGATTTGCTGCGCACCGATCCCGATTCCCGGCGCATCATCGTGTCGGCCTGGAACGTCGGCGA disruptive_inframe_deletion 0.97
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 0.11
clpC1 4040841 c.-138delG upstream_gene_variant 0.97
embC 4240418 p.Gly186Cys missense_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246088 c.-426A>G upstream_gene_variant 0.95
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
thyA 3074061 c.338_410delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA frameshift_variant 1.0