TB-Profiler result

Run: SRR6824581

Summary

Run ID: SRR6824581

Sample name:

Date: 20-10-2023 19:29:11

Number of reads: 7163280

Percentage reads mapped: 99.43

Strain: lineage2.2.2;lineage2.2.1

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
Rifampicin R rpoB p.His445Asp (0.14)
Isoniazid R katG p.Ser315Asn (0.15), ahpC c.-48G>A (0.12)
Ethambutol R embB p.Met306Ile (0.19)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.16), gid c.574_575delGG (0.85)
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
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 0.85
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.14
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.His445Asp missense_variant 0.14 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.16 streptomycin
katG 2155168 p.Ser315Asn missense_variant 0.15 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 0.12 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.19 ethambutol
gid 4407627 c.574_575delGG frameshift_variant 0.85 streptomycin
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 5908 c.669C>T synonymous_variant 0.81
gyrA 6649 c.-653T>C upstream_gene_variant 0.86
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
rpoB 760394 c.588C>T synonymous_variant 0.15
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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305417 c.2487C>T synonymous_variant 0.85
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834845 c.1313_1315delCCG disruptive_inframe_deletion 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154239 p.Thr625Ala missense_variant 0.89
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065914 p.Leu93Arg missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339564 c.447G>A synonymous_variant 0.81
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039778 c.927A>G synonymous_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246561 c.48T>C synonymous_variant 0.21
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338365 p.Cys53Arg missense_variant 0.16
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