TB-Profiler result

Run: SRR6650423
Summary

Run ID: SRR6650423

Sample name:

Date: 15-08-2023 08:05:40

Number of reads: 2492038

Percentage reads mapped: 99.41

Strain: lineage3

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Thr85Pro (0.24)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
katG 2155859 p.Thr85Pro missense_variant 0.24 isoniazid
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 490751 c.-32T>G upstream_gene_variant 0.25
fgd1 490771 c.-12T>G upstream_gene_variant 0.24
fgd1 491014 p.Thr78Pro missense_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.31
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763629 p.Val87Ala missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779363 p.Leu125Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.26
fbiC 1303016 p.Val29Gly missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.23
rrl 1475358 n.1701T>G non_coding_transcript_exon_variant 0.21
fabG1 1674076 p.Thr213Pro missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169862 p.Asn251His missense_variant 0.15
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
ahpC 2726338 p.Val49Gly missense_variant 0.33
ahpC 2726341 p.Val50Gly missense_variant 0.34
pepQ 2859377 p.Thr348Ala missense_variant 0.26
ribD 2986648 c.-191T>G upstream_gene_variant 0.2
Rv2752c 3064745 p.Thr483Pro missense_variant 0.38
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339736 p.Thr207Pro missense_variant 0.25
Rv3083 3449474 p.Phe324Ser missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642772 p.Asp413Gly missense_variant 0.26
alr 3841473 c.-53G>A upstream_gene_variant 1.0
alr 3841509 c.-89A>C upstream_gene_variant 0.24
ddn 3986997 p.Thr52Pro missense_variant 0.24
embC 4239973 c.111T>G synonymous_variant 0.23
embC 4241433 p.Met524Arg missense_variant 0.21
embC 4241445 p.Asp528Ala missense_variant 0.24
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269864 c.-31C>G upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0