TB-Profiler result

Run: SRR6650206
Summary

Run ID: SRR6650206

Sample name:

Date: 15-08-2023 08:02:32

Number of reads: 3506213

Percentage reads mapped: 99.23

Strain: lineage1.1.3.1

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.Ala281Val (1.00)
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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.99
lineage1.1.3.1 Indo-Oceanic NA RD239 0.97
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 2155270 p.Ala281Val missense_variant 1.0 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
gyrB 5117 c.-123G>A upstream_gene_variant 0.33
gyrB 5121 c.-119A>T upstream_gene_variant 0.25
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9315 c.2014C>T synonymous_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.25
fgd1 491014 p.Thr78Pro missense_variant 0.26
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576735 p.Leu463Arg missense_variant 0.18
mshA 576744 p.Val466Gly missense_variant 0.24
rpoB 759615 c.-192A>C upstream_gene_variant 0.23
rpoB 759620 c.-187A>C upstream_gene_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 763884 p.Ala172Val missense_variant 0.97
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777441 p.Val347Ala missense_variant 0.2
mmpL5 777572 c.909C>T synonymous_variant 0.97
mmpR5 779363 p.Leu125Arg missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.31
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154362 p.Phe584Val missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155856 p.Thr86Pro missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.14
PPE35 2169862 p.Asn251His missense_variant 0.24
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.21
Rv1979c 2222308 p.Asp286Gly missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.97
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94
ahpC 2726338 p.Val49Gly missense_variant 0.32
ahpC 2726341 p.Val50Gly missense_variant 0.3
ahpC 2726350 p.Trp53Leu missense_variant 0.18
pepQ 2859904 p.Val172Gly missense_variant 0.35
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064745 p.Thr483Pro missense_variant 0.31
thyX 3067995 c.-50A>C upstream_gene_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.29
fbiD 3339688 p.Thr191Pro missense_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.95
fprA 3475159 p.Asn385Asp missense_variant 0.97
Rv3236c 3612835 c.282T>G synonymous_variant 0.21
fbiB 3642751 p.Asp406Ala missense_variant 0.24
alr 3841253 c.168C>T synonymous_variant 0.98
alr 3841277 c.144C>T synonymous_variant 0.98
alr 3841506 c.-86A>C upstream_gene_variant 0.28
clpC1 4040517 p.Val63Ala missense_variant 0.98
embC 4239832 c.-31T>G upstream_gene_variant 0.2
embC 4239838 c.-25T>C upstream_gene_variant 0.36
embC 4239842 c.-21C>A upstream_gene_variant 0.24
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.27
embA 4243848 p.Val206Met missense_variant 0.98
embA 4245969 p.Pro913Ser missense_variant 0.97
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248452 p.Trp647Gly missense_variant 0.21
embB 4249305 p.Asn931Thr missense_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 0.97
ethA 4326019 c.1455C>T synonymous_variant 0.97
ethA 4328409 c.-936T>G upstream_gene_variant 0.23
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407780 c.423G>A synonymous_variant 0.94
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0