TB-Profiler result

Run: SRR25827856

Summary

Run ID: SRR25827856

Sample name:

Date: 02-02-2024 22:35:15

Number of reads: 8468230

Percentage reads mapped: 92.37

Strain: lineage3;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.Asp435Val (0.21), rpoB p.Ser450Leu (0.76)
Isoniazid R katG p.Ser315Thr (0.41)
Ethambutol R embB p.Met306Val (0.41), embB p.Gly406Ser (0.53)
Pyrazinamide R pncA p.Leu159Arg (0.46)
Streptomycin R rpsL p.Lys43Arg (0.36)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine R mmpR5 c.198dupG (0.36)
Para-aminosalicylic_acid
Delamanid
Bedaquiline R mmpR5 c.198dupG (0.36)
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.54
lineage2 East-Asian Beijing RD105 0.44
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.45
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.46
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 761110 p.Asp435Val missense_variant 0.21 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.76 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.36 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 0.36 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.41 isoniazid
pncA 2288766 p.Leu159Arg missense_variant 0.46 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.41 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.53 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 1.0
fgd1 491290 p.Val170Met missense_variant 0.53
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.42
ccsA 620625 p.Ile245Met missense_variant 0.42
rpoB 759746 c.-61C>T upstream_gene_variant 0.63
rpoB 760361 c.555T>C synonymous_variant 0.17
rpoB 760370 c.564C>G synonymous_variant 0.16
rpoB 760376 p.Asp190Glu missense_variant 0.16
rpoC 762434 c.-936T>G upstream_gene_variant 0.63
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763040 c.-330C>G upstream_gene_variant 0.15
rpoC 764566 c.1197C>G synonymous_variant 0.16
rpoC 764575 c.1206T>G synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.35
mmpS5 779615 c.-710C>G upstream_gene_variant 0.43
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800612 c.-197A>G upstream_gene_variant 0.16
rplC 800618 c.-191T>C upstream_gene_variant 0.16
rplC 800648 c.-161A>T upstream_gene_variant 0.18
rplC 800654 c.-155T>C upstream_gene_variant 0.16
rplC 800693 c.-116A>G upstream_gene_variant 0.16
rplC 800703 c.-106T>C upstream_gene_variant 0.16
Rv1258c 1406760 c.580_581insC frameshift_variant 0.42
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.2
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.19
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.19
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.19
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.18
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.19
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.22
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.25
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.24
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.24
rrl 1474960 n.1303C>G non_coding_transcript_exon_variant 0.17
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.19
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.18
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.18
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.18
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.18
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.18
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.18
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.19
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.24
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.23
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.21
rpsA 1834000 c.459G>C synonymous_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.56
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 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.58
pncA 2289365 c.-125delC upstream_gene_variant 0.49
ahpC 2726105 c.-88G>A upstream_gene_variant 0.52
pepQ 2860448 c.-30C>A upstream_gene_variant 0.56
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087756 p.Leu313Met missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.38
rpoA 3878416 p.Gly31Ala missense_variant 0.41
embC 4241022 p.Ala387Val missense_variant 0.43
embC 4242075 p.Arg738Gln missense_variant 0.52
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.49
embB 4247028 p.Leu172Arg missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.44
gid 4407927 p.Glu92Asp missense_variant 0.38