TB-Profiler result

Run: ERR4796555

Summary

Run ID: ERR4796555

Sample name:

Date: 01-04-2023 06:55:59

Number of reads: 3574926

Percentage reads mapped: 99.54

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 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.21 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289190 c.51dupC frameshift_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4327162 c.311delT frameshift_variant 0.83 ethionamide
gid 4407896 p.Glu103* stop_gained 1.0 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576482 p.Val379Leu missense_variant 0.21
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761465 c.1659G>A synonymous_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764293 c.924G>C synonymous_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475680 n.2023A>G non_coding_transcript_exon_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
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3065644 p.Thr183Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087292 c.474dupG frameshift_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243201 c.-31delC upstream_gene_variant 1.0
embA 4243440 c.208C>T synonymous_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.19
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.19
embB 4246563 p.Leu17Trp missense_variant 0.15
embB 4246567 c.54G>T synonymous_variant 0.16
ethA 4326543 p.Glu311* stop_gained 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407594 c.609G>A synonymous_variant 1.0