TB-Profiler result

Run: DRR130241
Summary

Run ID: DRR130241

Sample name:

Date: 31-03-2023 07:12:18

Number of reads: 3995538

Percentage reads mapped: 99.5

Strain: 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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
thyA 3074224 p.Trp83* stop_gained 1.0 para-aminosalicylic_acid
alr 3841409 p.Phe4Leu missense_variant 0.52 cycloserine
pncA 2287447 c.-701_*1233del 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 762286 p.Arg827Leu missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767007 p.Ala1213Glu missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473893 n.236T>C non_coding_transcript_exon_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918307 p.Arg123Leu missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154874 p.Tyr413Cys missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289941 c.-700C>G upstream_gene_variant 1.0
pncA 2289959 c.-718A>G upstream_gene_variant 0.11
thyX 3067960 c.-16_-15insC upstream_gene_variant 0.14
thyX 3067988 c.-43A>C upstream_gene_variant 0.53
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087693 c.877_878dupAC frameshift_variant 0.22
ald 3087700 p.Leu294Gln missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
alr 3841362 p.Thr20Met missense_variant 0.24
embC 4239918 p.Val19Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243201 c.-31delC upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326474 p.Pro334Ala missense_variant 1.0
ethA 4326923 p.Gly184Asp missense_variant 1.0
whiB6 4338365 p.Cys53Gly missense_variant 1.0
whiB6 4338504 c.18G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0