TB-Profiler result

Run: SRR6650198
Summary

Run ID: SRR6650198

Sample name:

Date: 15-08-2023 07:57:53

Number of reads: 507011

Percentage reads mapped: 99.62

Strain: lineage3

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 R pncA p.Thr177Pro (0.27)
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
pncA 2288713 p.Thr177Pro missense_variant 0.27 pyrazinamide
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 6645 p.Ser469Asn 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 490975 p.Thr65Pro missense_variant 0.2
fgd1 491014 p.Thr78Pro missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576590 p.Arg415Gly missense_variant 0.2
ccsA 619707 c.-184T>G upstream_gene_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759806 c.-1C>T upstream_gene_variant 0.22
rpoB 759816 p.Ser4Pro missense_variant 0.2
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 775643 c.2838A>C synonymous_variant 0.21
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778239 p.Val81Gly missense_variant 0.22
mmpL5 778907 c.-427C>G upstream_gene_variant 0.22
mmpR5 779336 p.Asp116Ala missense_variant 0.2
rpsL 781363 c.-197T>G upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781524 c.-36C>A upstream_gene_variant 0.25
rpsL 781526 c.-34G>A upstream_gene_variant 0.15
rpsL 781531 c.-29T>G upstream_gene_variant 0.17
rplC 801279 c.471G>C synonymous_variant 0.18
rplC 801287 p.Val160Gly missense_variant 0.3
fbiC 1303016 p.Val29Gly missense_variant 0.22
Rv1258c 1406452 p.Thr297Pro missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.27
rrl 1473921 n.264A>G non_coding_transcript_exon_variant 0.4
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.38
rrl 1473940 n.283A>C non_coding_transcript_exon_variant 0.33
rrl 1473945 n.288T>G non_coding_transcript_exon_variant 0.4
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.45
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.55
rrl 1473973 n.316T>G non_coding_transcript_exon_variant 0.2
inhA 1673679 c.-523T>G upstream_gene_variant 0.43
fabG1 1673690 p.Val84Gly missense_variant 0.29
fabG1 1674038 p.Gln200Arg missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918015 p.Leu26Val missense_variant 0.22
tlyA 1918391 p.Val151Gly missense_variant 0.22
tlyA 1918421 p.Ala161Gly missense_variant 0.21
tlyA 1918431 p.Leu164Phe missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169845 p.Asn256Lys missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288951 c.291T>G synonymous_variant 0.2
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.33
kasA 2518151 p.Ser13Arg missense_variant 0.4
kasA 2518605 p.Val164Gly missense_variant 0.6
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726255 c.63T>G synonymous_variant 0.25
folC 2746153 c.1446C>T synonymous_variant 0.18
folC 2746156 p.Leu481Phe missense_variant 0.18
pepQ 2859353 p.Gly356Arg missense_variant 0.22
pepQ 2859358 p.Thr354Asn missense_variant 0.22
pepQ 2859367 p.Met351Lys missense_variant 0.3
pepQ 2859377 p.Thr348Ala missense_variant 0.3
pepQ 2859425 p.Gly332Arg missense_variant 0.2
pepQ 2859445 p.Glu325Gly missense_variant 0.2
pepQ 2859448 p.Val324Gly missense_variant 0.27
pepQ 2859454 p.Val322Gly missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.44
fbiD 3339279 c.162T>G synonymous_variant 0.5
fbiD 3339281 p.Ser55Leu missense_variant 0.38
fbiD 3339303 c.186C>T synonymous_variant 0.22
fbiD 3339327 c.210T>G synonymous_variant 0.33
Rv3083 3449072 p.Val190Gly missense_variant 0.29
Rv3083 3449079 p.Leu192Phe missense_variant 0.25
Rv3083 3449083 p.Pro194Ser missense_variant 0.29
Rv3083 3449089 p.Met196Val missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612557 p.Val187Gly missense_variant 0.25
Rv3236c 3612569 p.Val183Gly missense_variant 0.25
fbiB 3642744 p.Ala404Ser missense_variant 0.18
fbiB 3642797 p.Leu421Phe missense_variant 0.22
alr 3841473 c.-53G>A upstream_gene_variant 1.0
ddn 3986763 c.-81A>G upstream_gene_variant 0.33
clpC1 4039471 p.Ile412Val missense_variant 0.29
embC 4239973 c.111T>G synonymous_variant 0.2
embC 4240001 p.Thr47Pro missense_variant 0.2
embC 4240006 c.144A>C synonymous_variant 0.3
embC 4240017 p.Val52Gly missense_variant 0.3
embC 4240044 p.Trp61Leu missense_variant 0.17
embC 4241421 p.Glu520Gly missense_variant 0.23
embC 4241423 p.Arg521Gly missense_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242422 p.Trp854Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.18
embC 4242831 p.Ala990Gly missense_variant 0.18
embC 4242908 p.Phe1016Val missense_variant 0.18
embA 4243332 p.Leu34Phe missense_variant 0.19
embA 4243347 p.Thr39Pro missense_variant 0.23
embA 4243350 p.Thr40Pro missense_variant 0.25
embA 4243361 c.129C>T synonymous_variant 0.17
embA 4243367 p.Trp45Cys missense_variant 0.25
embA 4243372 p.Gln47Arg missense_variant 0.36
embA 4243378 p.Ser49Thr missense_variant 0.18
embA 4243380 p.Thr50Pro missense_variant 0.18
embA 4244783 c.1551C>T synonymous_variant 1.0
embB 4247614 c.1101T>G synonymous_variant 0.36
embB 4247616 p.Glu368Gly missense_variant 0.27
embB 4247623 c.1110G>C synonymous_variant 0.2
embB 4248663 p.Val717Gly missense_variant 0.2
embB 4248689 p.Ile726Val missense_variant 0.3
embB 4249403 p.Thr964Pro missense_variant 0.29
aftB 4268776 p.Ser21Gly missense_variant 0.38
aftB 4268783 c.54C>G synonymous_variant 0.25
aftB 4268786 c.51C>T synonymous_variant 0.29
aftB 4268793 p.Val15Gly missense_variant 0.33
ubiA 4269864 c.-31C>G upstream_gene_variant 0.21
ethA 4326846 p.Thr210Pro missense_variant 0.15
ethR 4326874 c.-675C>T upstream_gene_variant 0.2
ethR 4326880 c.-669G>C upstream_gene_variant 0.4
ethA 4326887 p.Asp196Gly missense_variant 0.44
ethA 4326890 p.Ala195Gly missense_variant 0.18
ethR 4326898 c.-651C>G upstream_gene_variant 0.18
ethA 4326905 p.Leu190Pro missense_variant 0.18
ethR 4326907 c.-642C>G upstream_gene_variant 0.36
ethR 4327768 p.Thr74Pro missense_variant 0.2
ethR 4327784 p.Val79Gly missense_variant 0.17
ethR 4327813 p.Thr89Pro missense_variant 0.3
ethR 4328041 p.Thr165Pro missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0