TB-Profiler result

Run: ERR4800153
Summary

Run ID: ERR4800153

Sample name:

Date: 01-04-2023 09:37:41

Number of reads: 2547492

Percentage reads mapped: 99.43

Strain: 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 0.99
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 7570 p.Ala90Val missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.99 pyrazinamide
ethA 4327267 p.Trp69* stop_gained 0.96 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 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779287 p.Phe100Ile missense_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303271 p.Leu114Arg missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222418 p.Asp249Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.99
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449562 c.1059G>A synonymous_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841420 p.Val1Met missense_variant 1.0
panD 4044159 c.123C>A synonymous_variant 0.96
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.98
embA 4243539 p.Ala103Ser missense_variant 1.0
embA 4245263 p.Lys677Asn missense_variant 0.99
aftB 4269051 c.-215C>T upstream_gene_variant 1.0
ethR 4326727 c.-822C>A upstream_gene_variant 0.95
whiB6 4338468 c.54C>T synonymous_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4407868 p.Val112Gly missense_variant 0.96