TB-Profiler result

Run: SRR18910193
Summary

Run ID: SRR18910193

Sample name:

Date: 03-04-2023 20:38:59

Number of reads: 186938

Percentage reads mapped: 99.62

Strain: lineage2.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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
katG 2154109 p.Trp668* stop_gained 0.25 isoniazid
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759843 p.Pro13Thr missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766482 p.Arg1038Leu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775771 p.Ala904Ser missense_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777626 c.855C>T synonymous_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473012 n.1167G>T non_coding_transcript_exon_variant 0.13
rpsA 1833941 p.Val134Ile missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103233 c.-191G>T upstream_gene_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170340 p.Gln91His missense_variant 0.13
PPE35 2170392 p.Gly74Ala missense_variant 0.18
PPE35 2170400 c.213G>C synonymous_variant 0.18
Rv1979c 2222085 c.1080G>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517968 c.-147T>C upstream_gene_variant 0.25
ahpC 2726338 p.Val49Glu missense_variant 0.22
ahpC 2726422 p.Asp77Gly missense_variant 0.2
Rv2752c 3064723 p.Pro490Leu missense_variant 0.22
Rv2752c 3066994 c.-803A>G upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086957 c.138C>G synonymous_variant 0.33
Rv3083 3448374 c.-130A>G upstream_gene_variant 0.2
Rv3083 3449435 p.Ser311* stop_gained 0.22
Rv3083 3449749 p.Asn416Asp missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641436 c.-99T>A upstream_gene_variant 0.15
alr 3841149 p.Val91Ala missense_variant 0.25
alr 3841436 c.-16G>A upstream_gene_variant 0.17
clpC1 4039439 c.1266C>G synonymous_variant 0.18
clpC1 4039522 c.1183C>T synonymous_variant 0.14
clpC1 4040001 p.His235Ala missense_variant 0.2
clpC1 4040010 p.Ala232Arg missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243470 p.Ala80Ser missense_variant 0.17
embB 4247139 p.Arg209Leu missense_variant 0.15
embB 4249757 p.Thr1082Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4326967 c.-582C>T upstream_gene_variant 0.11
ethA 4327316 p.Ile53Thr missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408127 p.Leu26Val missense_variant 0.22
gid 4408373 c.-171C>A upstream_gene_variant 0.22
gid 4408469 c.-267T>A upstream_gene_variant 0.4