TB-Profiler result

Run: SRR6650108
Summary

Run ID: SRR6650108

Sample name:

Date: 15-08-2023 07:55:29

Number of reads: 299013

Percentage reads mapped: 99.29

Strain: lineage1.1.3

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.98
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.98
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 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 575165 c.-183C>T upstream_gene_variant 0.5
mshA 575739 p.Ala131Val missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.22
ccsA 620537 p.Val216Gly missense_variant 0.25
ccsA 620756 p.Asp289Gly missense_variant 0.22
ccsA 620763 c.873G>A synonymous_variant 0.22
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 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 777572 c.909C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.22
embR 1417010 p.Gly113Ala missense_variant 0.33
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 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918029 c.90C>A synonymous_variant 0.29
tlyA 1918031 p.Lys31Arg missense_variant 0.29
tlyA 1918134 c.195C>T synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169317 c.1296C>T synonymous_variant 0.5
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.5
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
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.4
ahpC 2726341 p.Val50Gly missense_variant 0.4
ahpC 2726350 p.Trp53Leu missense_variant 0.4
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087498 p.Gly227Ser missense_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.29
fbiD 3339310 p.Asp65His missense_variant 0.33
fbiD 3339688 p.Thr191Pro missense_variant 0.33
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 0.83
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642772 p.Asp413Ala missense_variant 0.4
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.5
embC 4239993 p.Ala44Gly missense_variant 0.33
embC 4240006 c.144A>C synonymous_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.57
embA 4242406 c.-827A>C upstream_gene_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249403 p.Thr964Pro missense_variant 1.0
aftB 4268233 p.Ile202Val missense_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269848 c.-15A>G upstream_gene_variant 0.3
ubiA 4269859 c.-26A>C upstream_gene_variant 0.2
ubiA 4269864 c.-31C>G upstream_gene_variant 0.18
ethR 4328041 p.Thr165Pro missense_variant 0.4
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407631 c.571delT frameshift_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0