TB-Profiler result

Run: ERR5897078
Summary

Run ID: ERR5897078

Sample name:

Date: 02-04-2023 00:47:35

Number of reads: 10723846

Percentage reads mapped: 99.59

Strain: lineage4.9;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.1
lineage4 Euro-American LAM;T;S;X;H None 0.89
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.09
lineage4.9 Euro-American (H37Rv-like) T1 None 0.9
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.11
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 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.94 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.16 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674048 c.-154G>A upstream_gene_variant 0.9 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288764 p.Thr160Pro missense_variant 0.11 pyrazinamide
pncA 2289081 p.Pro54Leu missense_variant 0.89 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327081 c.392delG frameshift_variant 1.0 ethionamide, 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
gyrA 7585 p.Ser95Thr missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 0.12
mshA 576400 c.1053C>T synonymous_variant 0.91
rpoB 761461 p.Arg552Leu missense_variant 0.9
rpoC 766645 p.Glu1092Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12
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
ndh 2102295 p.Thr250Ala missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.15
ald 3086987 p.Gln56His missense_variant 0.9
ald 3087367 p.Ala183Val missense_variant 0.92
ald 3087711 p.Val298Met missense_variant 0.94
Rv3236c 3612813 p.Thr102Ala missense_variant 0.12
rpoA 3877536 c.972C>T synonymous_variant 0.9
aftB 4267647 p.Asp397Gly missense_variant 0.12
ubiA 4269124 p.Ala237Val missense_variant 0.93
ethA 4328448 c.-975A>G upstream_gene_variant 0.12
whiB6 4338307 p.Ala72Gly missense_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0