TB-Profiler result

Run: SRR6650350
Summary

Run ID: SRR6650350

Sample name:

Date: 15-08-2023 07:36:30

Number of reads: 814917

Percentage reads mapped: 99.55

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 (0.19)
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 0.19 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
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 491008 p.Thr76Pro missense_variant 0.2
fgd1 491014 p.Thr78Pro missense_variant 0.22
fgd1 491027 p.Asn82Thr missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576489 p.Val381Gly missense_variant 0.2
mshA 576723 p.Val459Gly missense_variant 0.33
ccsA 619844 c.-47T>G upstream_gene_variant 0.19
ccsA 620748 c.858T>G synonymous_variant 0.26
ccsA 620752 p.Arg288Gly missense_variant 0.17
ccsA 620756 p.Asp289Gly missense_variant 0.32
ccsA 620773 p.Ile295Val missense_variant 0.24
rpoB 759611 c.-196G>C upstream_gene_variant 0.22
rpoB 759615 c.-192A>C upstream_gene_variant 0.56
rpoB 759620 c.-187A>C upstream_gene_variant 0.56
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
mmpR5 779348 p.Val120Gly missense_variant 0.25
mmpR5 779363 p.Leu125Arg missense_variant 0.36
mmpR5 779369 p.Asp127Ala missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781524 c.-36C>A upstream_gene_variant 0.29
rplC 801287 p.Val160Gly missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471710 n.-136T>G upstream_gene_variant 0.25
rrl 1473948 n.291C>A non_coding_transcript_exon_variant 0.29
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.29
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918394 p.Val152Gly missense_variant 0.25
ndh 2102509 c.534T>G synonymous_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.46
ndh 2103235 c.-193C>G upstream_gene_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169278 c.1335T>G synonymous_variant 0.25
PPE35 2169308 c.1305C>G synonymous_variant 0.25
PPE35 2169314 p.Asn433Lys missense_variant 0.2
PPE35 2169317 c.1296C>T synonymous_variant 0.2
PPE35 2170072 p.Gly181Arg missense_variant 0.14
PPE35 2170425 p.Val63Gly missense_variant 0.2
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
kasA 2518147 c.33C>T synonymous_variant 0.26
kasA 2518151 p.Ser13Arg missense_variant 0.22
kasA 2518605 p.Val164Gly missense_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.25
ahpC 2726286 p.Gly32Arg missense_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.21
fbiD 3339688 p.Thr191Pro missense_variant 0.3
Rv3083 3449089 p.Met196Val missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642751 p.Asp406Ala missense_variant 0.22
fbiB 3642772 p.Asp413Ala missense_variant 0.2
alr 3841473 c.-53G>A upstream_gene_variant 1.0
ddn 3986929 p.Tyr29Ser missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.22
embA 4242406 c.-827A>C upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244350 p.Leu373Pro missense_variant 1.0
embB 4247125 c.612G>C synonymous_variant 0.13
embB 4247173 c.660G>T synonymous_variant 0.13
embB 4247623 c.1110G>C synonymous_variant 0.38
embB 4249323 p.Ala937Glu missense_variant 0.33
aftB 4267843 p.Asp332Asn missense_variant 0.15
aftB 4268758 p.Ile27Val missense_variant 0.17
aftB 4268776 p.Ser21Gly missense_variant 0.23
ubiA 4269460 p.Ala125Gly missense_variant 0.22
ubiA 4269479 p.Met119Val missense_variant 0.33
aftB 4269486 c.-650T>G upstream_gene_variant 0.5
aftB 4269504 c.-668A>G upstream_gene_variant 0.4
ubiA 4269511 p.Val108Gly missense_variant 0.33
ubiA 4269856 c.-23G>A upstream_gene_variant 0.25
ethA 4326903 p.Val191Leu missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0