TB-Profiler result

Run: SRR6650323
Summary

Run ID: SRR6650323

Sample name:

Date: 15-08-2023 07:37:35

Number of reads: 1675171

Percentage reads mapped: 99.32

Strain: lineage1.2.2.2

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R gid c.115delC (1.00)
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 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 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
gid 4408087 c.115delC frameshift_variant 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
gyrB 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 5530 c.291C>T synonymous_variant 1.0
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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576723 p.Val459Gly missense_variant 0.22
ccsA 620770 p.Trp294Arg missense_variant 0.14
ccsA 620773 p.Ile295Val missense_variant 0.19
rpoB 759620 c.-187A>C upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779371 p.Ala128Pro missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.28
rplC 801302 p.Arg165Pro missense_variant 0.18
fbiC 1303016 p.Val29Gly missense_variant 0.19
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.25
rrl 1474469 n.812T>G non_coding_transcript_exon_variant 0.2
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.33
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.33
rrl 1476170 n.2513C>A non_coding_transcript_exon_variant 0.22
fabG1 1673690 p.Val84Gly missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918052 p.Pro38Arg missense_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.27
ndh 2103235 c.-193C>G upstream_gene_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.95
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714566 p.Leu256Pro missense_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
thyA 3074430 c.42G>A synonymous_variant 1.0
thyA 3074641 c.-170C>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
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 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642772 p.Asp413Ala missense_variant 0.24
alr 3841506 c.-86A>C upstream_gene_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241809 c.1947A>G synonymous_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.35
embA 4242406 c.-827A>C upstream_gene_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249322 p.Ala937Lys missense_variant 0.2
aftB 4268245 p.Ile198Val missense_variant 0.21
aftB 4268776 p.Ser21Gly missense_variant 0.25
aftB 4268786 c.51C>T synonymous_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269502 p.Val111Gly missense_variant 0.28
aftB 4269504 c.-668A>G upstream_gene_variant 0.34
ubiA 4269511 p.Val108Gly missense_variant 0.29
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4326898 c.-651C>G upstream_gene_variant 0.17
ethA 4326905 p.Leu190Pro missense_variant 0.15
ethA 4328193 c.-720G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0