TB-Profiler result

Run: ERR8975165

Summary

Run ID: ERR8975165

Sample name:

Date: 02-04-2023 08:42:46

Number of reads: 2959097

Percentage reads mapped: 99.6

Strain: lineage4.4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289179 c.62delT frameshift_variant 1.0 pyrazinamide, pyrazinamide
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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575552 p.Asn69Tyr missense_variant 0.12
mshA 576047 p.Arg234* stop_gained 0.11
rpoB 761601 p.Ala599Thr missense_variant 0.12
rpoC 764817 p.Val483Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303929 c.999G>T synonymous_variant 0.22
fbiC 1304089 p.Asp387Asn missense_variant 0.67
fbiC 1305419 p.Val830Ala missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2167819 p.Gly932Ser missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746267 c.1332C>T synonymous_variant 0.14
thyX 3067220 c.726G>T synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339194 p.Leu26Pro missense_variant 0.1
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475306 p.Gly434Ser missense_variant 0.17
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3642172 p.Pro213Leu missense_variant 1.0
embC 4241155 c.1293C>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243990 p.Ala253Val missense_variant 0.2
embA 4244670 p.Ala480Pro missense_variant 0.12
embB 4247798 p.Thr429Ala missense_variant 0.33
ubiA 4270032 c.-199C>T upstream_gene_variant 0.25
whiB6 4338594 c.-73T>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407714 p.Lys163Asn missense_variant 1.0