TB-Profiler result

Run: SRR6650193
Summary

Run ID: SRR6650193

Sample name:

Date: 15-08-2023 08:20:24

Number of reads: 1517698

Percentage reads mapped: 99.54

Strain: lineage3

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
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
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 6918 p.His560Leu missense_variant 0.15
gyrA 6922 c.-380G>T upstream_gene_variant 0.2
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 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.17
ccsA 619849 c.-42G>C upstream_gene_variant 0.16
ccsA 620748 c.858T>G synonymous_variant 0.28
ccsA 620756 p.Asp289Gly missense_variant 0.21
ccsA 620773 p.Ile295Val missense_variant 0.2
rpoB 759611 c.-196G>C upstream_gene_variant 0.33
rpoB 759615 c.-192A>C upstream_gene_variant 0.38
rpoB 759620 c.-187A>C upstream_gene_variant 0.22
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461087 p.Leu15Val missense_variant 0.14
atpE 1461108 p.Ile22Leu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472499 n.654A>G non_coding_transcript_exon_variant 0.2
rrl 1474469 n.812T>A non_coding_transcript_exon_variant 0.15
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.22
tlyA 1917817 c.-123A>C upstream_gene_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918044 p.Asp35Glu missense_variant 0.2
tlyA 1918069 p.Thr44Pro missense_variant 0.19
ndh 2103225 c.-183A>C upstream_gene_variant 0.24
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167660 p.Thr985Pro missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167934 c.2679G>C synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288867 c.375C>A synonymous_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 2726277 p.Lys29Gln missense_variant 0.24
folC 2746168 c.1431G>C synonymous_variant 0.14
folC 2746184 p.Val472Gly missense_variant 0.18
pepQ 2860012 p.Asp136Gly missense_variant 0.15
ribD 2987323 p.Val162Gly missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339279 c.162T>G synonymous_variant 0.19
Rv3083 3448765 p.Thr88Pro missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.16
Rv3236c 3611983 c.1134G>C synonymous_variant 0.15
Rv3236c 3612569 p.Val183Gly missense_variant 0.17
Rv3236c 3612784 p.Leu111Phe missense_variant 0.17
Rv3236c 3613185 c.-69T>A upstream_gene_variant 0.12
fbiB 3642113 c.579A>C synonymous_variant 0.13
fbiB 3642764 p.Asp410Glu missense_variant 0.2
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4240006 c.144A>C synonymous_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.24
embA 4244187 p.Thr319Pro missense_variant 0.19
embA 4244911 p.Leu560Pro missense_variant 0.17
embA 4244922 p.Thr564Pro missense_variant 0.18
embB 4249323 p.Ala937Glu missense_variant 0.21
embB 4249398 p.Ala962Gly missense_variant 0.15
aftB 4268774 p.Ser21Gly missense_variant 0.19
ubiA 4269817 p.Val6Gly missense_variant 0.24
ethR 4326883 c.-666C>G upstream_gene_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407961 p.Ile81Thr missense_variant 1.0