TB-Profiler result

Run: ERR4828389
Summary

Run ID: ERR4828389

Sample name:

Date: 20-10-2023 13:47:49

Number of reads: 1878859

Percentage reads mapped: 99.44

Strain: lineage2.2.1.2;lineage1.1.1

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.29)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1034delA (0.45), ethA c.1034delA (0.45)
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 0.39
lineage1 Indo-Oceanic EAI RD239 0.63
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.63
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.4
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.41
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.64
lineage2.2.1.2 East-Asian (Beijing) Beijing-RD142 RD105;RD207;RD181;RD142 0.37
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 0.29 streptomycin
ethA 4326439 c.1034delA frameshift_variant 0.45 ethionamide, ethionamide
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 6112 p.Met291Ile missense_variant 0.53
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.72
gyrA 9143 c.1842T>C synonymous_variant 0.69
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.39
ccsA 620625 p.Ile245Met missense_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.61
rpoC 763886 c.517C>A synonymous_variant 0.61
rpoC 765171 p.Pro601Leu missense_variant 0.66
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.44
mmpL5 778855 c.-375G>C upstream_gene_variant 0.62
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.19
embR 1417019 p.Cys110Tyr missense_variant 0.65
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.56
rpsA 1834177 c.636A>C synonymous_variant 0.45
rpsA 1834319 p.Val260Ile missense_variant 0.54
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 2167983 p.Gly877Asp missense_variant 0.63
PPE35 2170466 c.147A>C synonymous_variant 0.56
Rv1979c 2222308 p.Asp286Gly missense_variant 0.55
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.61
ahpC 2726051 c.-142G>A upstream_gene_variant 0.59
Rv2752c 3064632 c.1560C>T synonymous_variant 0.59
thyA 3073768 p.Arg235Gln missense_variant 0.43
ald 3086750 c.-70A>C upstream_gene_variant 0.63
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.72
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.68
fprA 3475159 p.Asn385Asp missense_variant 0.6
Rv3236c 3612813 p.Thr102Ala missense_variant 0.36
clpC1 4040517 p.Val63Ala missense_variant 0.65
embC 4240671 p.Thr270Ile missense_variant 0.8
embC 4241042 p.Asn394Asp missense_variant 0.71
embA 4242388 c.-845C>T upstream_gene_variant 0.32
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.31
embA 4243848 p.Val206Met missense_variant 0.72
embA 4244096 c.864C>T synonymous_variant 0.62
embA 4245969 p.Pro913Ser missense_variant 0.52
embB 4247646 p.Glu378Ala missense_variant 0.71
aftB 4267647 p.Asp397Gly missense_variant 0.42
ubiA 4269387 p.Glu149Asp missense_variant 0.58
aftB 4269606 c.-770T>C upstream_gene_variant 0.64
whiB6 4338242 p.Gln94Glu missense_variant 0.51
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.57
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.54
gid 4407927 p.Glu92Asp missense_variant 0.41