TB-Profiler result

Run: SRR12142426
Summary

Run ID: SRR12142426

Sample name:

Date: 03-04-2023 06:27:59

Number of reads: 874112

Percentage reads mapped: 99.44

Strain: lineage2.2.2

Drug-resistance: MDR-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
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.99
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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.83 pyrazinamide, 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 491742 c.960T>C synonymous_variant 1.0
mshA 575941 c.594G>A synonymous_variant 0.11
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
mmpL5 777647 c.834C>T synonymous_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472508 n.663T>A non_coding_transcript_exon_variant 0.22
rrl 1476467 n.2810A>C non_coding_transcript_exon_variant 0.25
rrl 1476471 n.2814G>A non_coding_transcript_exon_variant 0.29
rrl 1476473 n.2816G>C non_coding_transcript_exon_variant 0.29
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167928 c.2685G>T synonymous_variant 1.0
Rv1979c 2222073 c.1092G>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518552 p.Met146Ile missense_variant 0.13
pepQ 2859594 c.825T>C synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407857 p.Arg116Trp missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0