TB-Profiler result

Run: ERR4553978
Summary

Run ID: ERR4553978

Sample name:

Date: 01-04-2023 06:27:27

Number of reads: 872427

Percentage reads mapped: 99.57

Strain: lineage4.1

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
lineage4.1 Euro-American T;X;H None 0.08
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 7581 p.Asp94Tyr 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 2288934 p.Tyr103Cys missense_variant 1.0 pyrazinamide
embB 4249583 p.Asp1024Asn 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 0.95
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.4
mshA 576609 p.Ala421Gly missense_variant 0.18
rpoB 759939 p.Pro45Ala missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339726 c.609A>T synonymous_variant 0.27
fbiD 3339734 p.Ala206Gly missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
alr 3840864 p.Asp186Gly missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878601 c.-95delG upstream_gene_variant 0.67
embC 4240390 p.Asn176Lys missense_variant 1.0
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242526 c.-707C>G upstream_gene_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248324 p.Ala604Gly missense_variant 0.3
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4326129 p.Gln449* stop_gained 1.0
ethA 4327161 p.Ile105Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407551 p.Met218Val missense_variant 1.0