TB-Profiler result

Run: ERR4797587
Summary

Run ID: ERR4797587

Sample name:

Date: 01-04-2023 07:46:01

Number of reads: 4087028

Percentage reads mapped: 99.55

Strain: lineage4.2

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
lineage4.2 Euro-American H;T;LAM 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 761140 p.His445Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288880 p.Arg121Pro missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247429 p.Met306Leu missense_variant 0.99 ethambutol
ethA 4326455 c.1016_1018delTTA disruptive_inframe_deletion 1.0 ethionamide
gid 4407830 p.Gln125* stop_gained 0.99 streptomycin
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
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.34
rpoC 762722 c.-648C>T upstream_gene_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
rrs 1472847 n.1002G>T non_coding_transcript_exon_variant 0.11
rrl 1474108 n.451C>A non_coding_transcript_exon_variant 0.13
rrl 1475063 n.1406A>C non_coding_transcript_exon_variant 0.33
rrl 1475518 n.1861A>G non_coding_transcript_exon_variant 1.0
inhA 1674135 c.-67C>T upstream_gene_variant 0.92
rpsA 1834689 p.Ser383Ile missense_variant 0.21
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878536 c.-29G>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246569 p.Ala19Val missense_variant 0.11
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4247028 p.Leu172Arg missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0