TB-Profiler result

Run: ERR4829940
Summary

Run ID: ERR4829940

Sample name:

Date: 01-04-2023 19:46:42

Number of reads: 2288611

Percentage reads mapped: 99.66

Strain: lineage4;lineage3

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
lineage3 East-African-Indian CAS RD750 0.22
lineage4 Euro-American LAM;T;S;X;H None 0.79
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 6738 p.Thr500Ile missense_variant 0.32 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Arg missense_variant 0.25 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 0.24 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.79 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.391dupG frameshift_variant 0.24 pyrazinamide, pyrazinamide
pncA 2289231 p.Leu4Ser missense_variant 0.75 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327328 c.145dupC frameshift_variant 0.33 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
gyrB 6061 p.Ser274Arg missense_variant 0.76
gyrB 6735 p.Asn499Ser missense_variant 0.68
gyrB 7210 p.Asp657Glu missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Ser missense_variant 0.6
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.28
mshA 576108 p.Ala254Gly missense_variant 0.21
rpoB 759628 c.-179C>T upstream_gene_variant 0.73
rpoC 762434 c.-936T>G upstream_gene_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.24
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407255 p.Ala29Glu missense_variant 0.8
rrs 1471653 n.-193C>T upstream_gene_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673393 c.-809G>A upstream_gene_variant 0.86
inhA 1673431 c.-771G>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 0.27
PPE35 2169779 c.834A>C synonymous_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289256 c.-15A>C upstream_gene_variant 0.83
pncA 2289365 c.-125delC upstream_gene_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 0.28
Rv2752c 3065855 p.Ala113Pro missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 0.24
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.24
fprA 3474299 p.Asp98Gly missense_variant 0.61
fprA 3474367 p.Gly121Ser missense_variant 0.75
panD 4043957 p.Asp109Asn missense_variant 0.72
panD 4044399 c.-118C>T upstream_gene_variant 0.28
embC 4242075 p.Arg738Gln missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268003 c.834G>A synonymous_variant 0.29
ethA 4328317 c.-844C>T upstream_gene_variant 0.78
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.24
gid 4408009 c.193delG frameshift_variant 0.24