TB-Profiler result

Run: SRR7592384
Summary

Run ID: SRR7592384

Sample name:

Date: 04-04-2023 19:51:14

Number of reads: 3630179

Percentage reads mapped: 99.46

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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
pncA 2289219 p.Asp8Ala missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Pro missense_variant 1.0 ethambutol
ethA 4326074 c.1014_1399del frameshift_variant 1.0 ethionamide
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
mshA 576108 p.Ala254Gly missense_variant 0.2
rpoC 765425 c.2059_2061dupCAG conservative_inframe_insertion 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781362 c.-198_-197insTAT upstream_gene_variant 0.8
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747468 p.Asp44Ile missense_variant 0.98
folC 2747470 p.Ile43Met missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.18
Rv2752c 3065335 p.Leu286Arg missense_variant 1.0
Rv2752c 3067110 c.-919A>G upstream_gene_variant 1.0
ald 3086822 c.3G>A start_lost 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.62
fbiD 3339744 c.627A>T synonymous_variant 0.33
fbiD 3339746 p.Ala210Gly missense_variant 0.37
rpoA 3878641 c.-134C>G upstream_gene_variant 0.69
embC 4240409 p.Pro183Ala missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.14
embB 4246567 c.54G>T synonymous_variant 0.12
embB 4246584 p.Arg24Pro missense_variant 0.4
ubiA 4269292 p.Ala181Val missense_variant 1.0
ethA 4326052 p.Asp474Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0