TB-Profiler result

Run: ERR11080930
Summary

Run ID: ERR11080930

Sample name:

Date: 07-04-2023 22:31:32

Number of reads: 6277006

Percentage reads mapped: 99.54

Strain: lineage4.1.1.3

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 7572 p.Ser91Pro missense_variant 0.48 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761100 p.Gln432Lys missense_variant 1.0 rifampicin
folC 2747454 p.Arg49Trp missense_variant 1.0 para-aminosalicylic_acid
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 1.0
gyrA 7571 c.270G>A synonymous_variant 0.48
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8105 c.804G>A synonymous_variant 1.0
gyrA 8164 p.Ala288Asp missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576404 p.Glu353* stop_gained 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766744 p.Gln1125His 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
katG 2155645 p.Gly156Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289250 c.-11_-10delAT upstream_gene_variant 1.0
folC 2746169 p.Ala477Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087192 c.376_377dupGC frameshift_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.24
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269271 p.Val188Ala missense_variant 1.0
ethA 4326330 p.Tyr382Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407980 p.Pro75Ser missense_variant 1.0