TB-Profiler result

Run: SRR21277283

Summary

Run ID: SRR21277283

Sample name:

Date: 04-04-2023 00:55:29

Number of reads: 13779881

Percentage reads mapped: 99.0

Strain: lineage4.4.2

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.2 Euro-American T1;T2 None 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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747481 p.Glu40Gln missense_variant 1.0 para-aminosalicylic_acid
embB 4248002 p.Gln497Lys missense_variant 0.99 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp 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
pncA 2289106 p.Ala46Thr missense_variant 1.0
pepQ 2860048 c.370dupG frameshift_variant 0.17
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
thyX 3067954 c.-9G>A upstream_gene_variant 0.99
thyA 3074336 p.Thr46Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087533 c.715delG frameshift_variant 0.65
fbiD 3339668 p.Gly184Val missense_variant 0.22
Rv3083 3449185 p.Glu228* stop_gained 0.5
Rv3083 3449566 p.Gly355Trp missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840463 p.Arg320Trp missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ethA 4327293 p.Thr61Ala missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407790 p.Ala138Val missense_variant 1.0
Rv3083 3448909 c.407_1120del disruptive_inframe_deletion 1.0