TB-Profiler result

Run: SRR6650394
Summary

Run ID: SRR6650394

Sample name:

Date: 15-08-2023 07:39:40

Number of reads: 908338

Percentage reads mapped: 99.6

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 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 6894 p.Met552Arg missense_variant 0.2
gyrB 6917 p.His560Tyr missense_variant 0.22
gyrA 6922 c.-380G>T upstream_gene_variant 0.38
gyrB 6929 p.Ala564Pro missense_variant 0.22
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 490751 c.-32T>G upstream_gene_variant 0.18
fgd1 490756 c.-27T>G upstream_gene_variant 0.18
fgd1 491008 p.Thr76Pro missense_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575155 c.-193T>G upstream_gene_variant 0.22
mshA 576723 p.Val459Gly missense_variant 0.2
ccsA 620537 p.Val216Gly missense_variant 0.2
ccsA 620545 p.Leu219Val missense_variant 0.25
ccsA 620551 p.Asp221His missense_variant 0.27
ccsA 620564 p.Leu225Pro missense_variant 0.17
ccsA 620567 p.Asp226Gly missense_variant 0.17
ccsA 620571 c.681A>G synonymous_variant 0.17
ccsA 620748 c.858T>G synonymous_variant 0.21
ccsA 620756 p.Asp289Gly missense_variant 0.24
ccsA 620770 p.Trp294Arg missense_variant 0.14
ccsA 620773 p.Ile295Val missense_variant 0.27
ccsA 620795 p.Ala302Gly missense_variant 0.19
rpoB 759611 c.-196G>C upstream_gene_variant 0.25
rpoB 759615 c.-192A>C upstream_gene_variant 0.29
rpoB 759620 c.-187A>C upstream_gene_variant 0.25
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.19
fbiC 1303016 p.Val29Gly missense_variant 0.25
fbiC 1303032 c.102A>C synonymous_variant 0.14
fbiC 1303038 c.108T>G synonymous_variant 0.21
Rv1258c 1407081 p.Ala87Gly missense_variant 0.43
atpE 1461086 c.42A>G synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.56
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.17
fabG1 1673178 c.-262G>A upstream_gene_variant 0.54
fabG1 1674076 p.Thr213Pro missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918004 p.Gln22Arg missense_variant 0.17
tlyA 1918010 p.Ala24Gly missense_variant 0.25
tlyA 1918031 p.Lys31Arg missense_variant 0.27
tlyA 1918061 p.Lys41Arg missense_variant 0.2
tlyA 1918066 p.Ala43Pro missense_variant 0.15
ndh 2103225 c.-183A>C upstream_gene_variant 0.38
ndh 2103235 c.-193C>G upstream_gene_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_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 2726338 p.Val49Gly missense_variant 0.2
ahpC 2726341 p.Val50Gly missense_variant 0.19
ahpC 2726350 p.Trp53Leu missense_variant 0.19
folC 2746657 c.942T>G synonymous_variant 0.14
folC 2746745 p.Val285Gly missense_variant 0.25
thyA 3074645 c.-174T>G upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3986919 p.Thr26Pro missense_variant 0.18
clpC1 4039471 p.Ile412Val missense_variant 0.19
embC 4240657 c.795G>C synonymous_variant 0.25
embC 4240661 p.Trp267Arg missense_variant 0.3
embC 4240667 p.Ser269Ala missense_variant 0.22
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.18
embA 4243365 p.Trp45Gly missense_variant 0.19
embB 4248663 p.Val717Gly missense_variant 0.18
embB 4249298 p.Trp929Gly missense_variant 0.15
embB 4249305 p.Asn931Thr missense_variant 0.25
embB 4249323 p.Ala937Glu missense_variant 0.33
aftB 4269486 c.-650T>G upstream_gene_variant 0.19
aftB 4269504 c.-668A>G upstream_gene_variant 0.25
ethR 4327637 p.Leu30Pro missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0