TB-Profiler result

Run: SRR8651660
Summary

Run ID: SRR8651660

Sample name:

Date: 04-04-2023 21:54:19

Number of reads: 10910077

Percentage reads mapped: 99.56

Strain: lineage4.4.2

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 0.98
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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Gly missense_variant 0.12 pyrazinamide
pncA 2288859 c.381_382dupGG frameshift_variant 0.14 pyrazinamide
pncA 2289016 p.Thr76Pro missense_variant 0.56 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol
embB 4247730 p.Gly406Ala 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760939 p.Leu378Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406745 p.Pro199Arg missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475953 n.2296A>C non_coding_transcript_exon_variant 0.89
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102035 c.1006_1007dupGC frameshift_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
thyX 3067743 p.Gly68Ala missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878637 c.-130G>C upstream_gene_variant 0.1
clpC1 4039873 p.Thr278Ser missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.98
embB 4247249 p.Gly246Arg missense_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 0.98
aftB 4269375 c.-539G>A upstream_gene_variant 0.98
ethA 4326632 p.His281Arg missense_variant 0.11
ethA 4327313 p.Arg54His missense_variant 0.56
ethA 4327350 p.Gly42Cys missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407961 p.Ile81Arg missense_variant 0.99