TB-Profiler result

Run: ERR4800228
Summary

Run ID: ERR4800228

Sample name:

Date: 01-04-2023 09:40:38

Number of reads: 7787966

Percentage reads mapped: 99.48

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 7582 p.Asp94Gly missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
ethA 4326419 c.1054delG frameshift_variant 1.0 ethionamide, ethionamide
gid 4407824 p.Gln127* stop_gained 0.98 streptomycin
pncA 2288551 c.-1186_*129del transcript_ablation 1.0 pyrazinamide
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575882 p.Thr179Ala missense_variant 0.99
mshA 576108 p.Ala254Gly missense_variant 0.16
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759786 c.-21G>C upstream_gene_variant 1.0
rpoB 759939 p.Pro45Thr missense_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779528 c.-627_-624delATCG upstream_gene_variant 0.98
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
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747195 p.Asp135Gly missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641802 p.Asp90Asn missense_variant 0.98
alr 3841473 c.-53G>A upstream_gene_variant 0.98
embC 4242075 p.Arg738Gln missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.15
embB 4247108 p.Gly199Arg missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408107 p.Glu32Asp missense_variant 0.97