TB-Profiler result

Run: ERR4830347
Summary

Run ID: ERR4830347

Sample name:

Date: 20-10-2023 13:15:47

Number of reads: 6446465

Percentage reads mapped: 96.97

Strain: lineage2.2.1;lineage1.1.1.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.10)
Ethambutol
Pyrazinamide
Streptomycin R gid c.471delG (0.76)
Fluoroquinolones R gyrB p.Ser447Phe (0.14)
Moxifloxacin R gyrB p.Ser447Phe (0.14)
Ofloxacin R gyrB p.Ser447Phe (0.14)
Levofloxacin R gyrB p.Ser447Phe (0.14)
Ciprofloxacin R gyrB p.Ser447Phe (0.14)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1034delA (0.12), ethA c.1034delA (0.12)
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 0.23
lineage1 Indo-Oceanic EAI RD239 0.75
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.77
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.22
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.24
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.74
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.68
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
gyrB 6579 p.Ser447Phe missense_variant 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2155168 p.Ser315Thr missense_variant 0.1 isoniazid
ethA 4326439 c.1034delA frameshift_variant 0.12 ethionamide, ethionamide
gid 4407731 c.471delG frameshift_variant 0.76 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 6112 p.Met291Ile missense_variant 0.75
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7466 c.165G>A synonymous_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.8
gyrA 9143 c.1842T>C synonymous_variant 0.72
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 0.66
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.77
rpoC 763886 c.517C>A synonymous_variant 0.76
rpoC 765171 p.Pro601Leu missense_variant 0.78
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 777581 p.Tyr300* stop_gained 0.68
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.76
rpsA 1834177 c.636A>C synonymous_variant 0.24
rpsA 1834319 p.Val260Ile missense_variant 0.72
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 0.73
Rv1979c 2222308 p.Asp286Gly missense_variant 0.77
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.78
ahpC 2726051 c.-142G>A upstream_gene_variant 0.82
ribD 2986925 c.87C>A synonymous_variant 0.11
Rv2752c 3064632 c.1560C>T synonymous_variant 0.79
thyA 3073768 p.Arg235Gln missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.69
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.76
fprA 3475159 p.Asn385Asp missense_variant 0.82
Rv3236c 3612813 p.Thr102Ala missense_variant 0.27
rpoA 3878630 c.-124delC upstream_gene_variant 0.67
clpC1 4040517 p.Val63Ala missense_variant 0.74
embC 4240411 c.549G>T synonymous_variant 0.74
embC 4240671 p.Thr270Ile missense_variant 0.79
embC 4241042 p.Asn394Asp missense_variant 0.77
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.2
embA 4243848 p.Val206Met missense_variant 0.81
embA 4244096 c.864C>T synonymous_variant 0.76
embA 4244837 c.1605G>C synonymous_variant 0.11
embA 4245969 p.Pro913Ser missense_variant 0.77
embB 4247646 p.Glu378Ala missense_variant 0.76
embB 4248195 p.Lys561Arg missense_variant 0.7
aftB 4267647 p.Asp397Gly missense_variant 0.23
ubiA 4269387 p.Glu149Asp missense_variant 0.72
aftB 4269606 c.-770T>C upstream_gene_variant 0.85
ethA 4326676 p.Ser266Arg missense_variant 0.26
whiB6 4338242 p.Gln94Glu missense_variant 0.76
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.73
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407870 c.333C>G synonymous_variant 0.13
gid 4407873 c.330G>T synonymous_variant 0.79
gid 4407927 p.Glu92Asp missense_variant 0.26