TB-Profiler result

Run: SRR6650182
Summary

Run ID: SRR6650182

Sample name:

Date: 15-08-2023 07:58:10

Number of reads: 751644

Percentage reads mapped: 99.17

Strain: lineage1

Drug-resistance: Sensitive

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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
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
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
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 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
fgd1 491008 p.Thr76Pro missense_variant 0.38
fgd1 491014 p.Thr78Pro missense_variant 0.25
fgd1 491027 p.Asn82Thr missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575165 c.-183C>T upstream_gene_variant 0.16
ccsA 620748 c.858T>G synonymous_variant 0.29
ccsA 620756 p.Asp289Gly missense_variant 0.26
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
rpoC 767011 c.3642G>C synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778239 p.Val81Gly missense_variant 0.33
mmpR5 779336 p.Asp116Ala missense_variant 0.29
mmpR5 779346 p.Asp119Glu missense_variant 0.25
mmpR5 779348 p.Val120Gly missense_variant 0.38
mmpR5 779363 p.Leu125Arg missense_variant 0.38
mmpR5 779369 p.Asp127Ala missense_variant 0.33
mmpR5 779371 p.Ala128Pro missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.22
embR 1416481 c.867G>A synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471981 n.136C>A 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 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.67
Rv1979c 2221725 c.1440T>G synonymous_variant 1.0
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 2714505 c.828C>T synonymous_variant 1.0
eis 2714559 c.774C>G synonymous_variant 0.18
eis 2714564 p.Ile257Val missense_variant 0.18
eis 2714566 p.Leu256Pro missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726269 p.Val26Gly missense_variant 0.33
pepQ 2859438 c.981T>G synonymous_variant 0.25
pepQ 2859454 p.Val322Gly missense_variant 0.18
ribD 2987320 p.Glu161Gly missense_variant 0.18
ribD 2987323 p.Val162Gly missense_variant 0.18
ribD 2987351 c.513C>G synonymous_variant 0.2
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087914 p.Glu365Asp missense_variant 0.25
fbiD 3339273 c.156T>G synonymous_variant 0.23
fbiD 3339279 c.162T>G synonymous_variant 0.31
fbiD 3339310 p.Asp65His missense_variant 0.25
fbiD 3339583 p.Thr156Pro missense_variant 0.31
fbiD 3339593 p.His159Pro missense_variant 0.25
fbiD 3339688 p.Thr191Pro missense_variant 0.2
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
Rv3236c 3612515 p.Arg201His missense_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 0.75
clpC1 4040517 p.Val63Ala missense_variant 1.0
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
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.4
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269486 c.-650T>G upstream_gene_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_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