TB-Profiler result

Run: ERR019572
Summary

Run ID: ERR019572

Sample name:

Date: 20-10-2023 23:27:36

Number of reads: 4137677

Percentage reads mapped: 92.51

Strain: lineage2.2.1

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
Rifampicin
Isoniazid R katG p.Ser315Thr (0.97)
Ethambutol R embA c.-12C>T (1.00), embB p.Met306Val (1.00)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (1.00)
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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.98
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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.97
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.96
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 0.97
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.11
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.1
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.1
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.41
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.41
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.18
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.45
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.51
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.28
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.34
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.31
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.34
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.32
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.29
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.23
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.21
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.17
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.19
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.19
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.19
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.28
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.27
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.25
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.38
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.48
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.52
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.48
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.48
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.63
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.53
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.57
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.57
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.46
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
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
Rv1979c 2222112 c.1052dupT frameshift_variant 0.98
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
ddn 3986931 p.Arg30Ser 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
ethR 4327870 p.Asn108Asp 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