TB-Profiler result

Run: ERR1213874
Summary

Run ID: ERR1213874

Sample name:

Date: 19-10-2023 20:50:44

Number of reads: 7628449

Percentage reads mapped: 99.06

Strain: 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.Ser450Leu (0.99)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA c.-224_*330del (0.99)
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
lineage2 East-Asian Beijing RD105 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
pncA 2288350 c.-224_*330del transcript_ablation 0.99 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 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
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 0.99
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473632 n.-26G>A upstream_gene_variant 1.0
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.25
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.3
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.31
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.28
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.16
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.15
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.28
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.25
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.16
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.18
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.19
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.17
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.17
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.19
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.22
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.16
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.17
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.16
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.12
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.11
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.15
rrl 1475289 n.1632G>A non_coding_transcript_exon_variant 0.16
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.16
rrl 1475297 n.1640C>T non_coding_transcript_exon_variant 0.2
rrl 1475315 n.1658A>C non_coding_transcript_exon_variant 0.23
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.11
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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
embC 4240423 c.561G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245966 p.Phe912Leu missense_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 4407927 p.Glu92Asp missense_variant 1.0