TB-Profiler result

Run: SRR6257024

Summary

Run ID: SRR6257024

Sample name:

Date: 18-08-2022 11:57:42

Number of reads: 722580

Percentage reads mapped: 99.66

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrB 6750 p.Ala504Val missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoC 764948 p.Leu527Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288953 p.Gly97Ser missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 6579 p.Ser447Tyr missense_variant 0.11
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
rpoB 759668 c.-139A>G upstream_gene_variant 0.14
rpoB 759783 c.-24C>T upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765571 c.2202C>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.13
rrl 1475761 n.2104C>T non_coding_transcript_exon_variant 0.17
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.11
fabG1 1674149 p.Ile237Asn missense_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155388 p.Met242Val missense_variant 0.09
ahpC 2726746 p.Leu185Gln missense_variant 0.15
folC 2746267 c.1332C>A synonymous_variant 0.12
ald 3086726 c.-94C>A upstream_gene_variant 0.12
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ddn 3986665 c.-179G>A upstream_gene_variant 0.1
ddn 3987118 p.Leu92Pro missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243336 p.Pro35Gln missense_variant 0.66
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
ethA 4327480 c.-7T>G upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0