TB-Profiler result

Run: ERR11465987
Summary

Run ID: ERR11465987

Sample name:

Date: 10-01-2024 06:40:28

Number of reads: 2215555

Percentage reads mapped: 99.35

Strain: lineage4.8.1;lineage1.2.2.2

Drug-resistance: Pre-XDR-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 R rpoB p.His445Leu (0.68)
Isoniazid R katG p.Ser315Thr (0.75)
Ethambutol R embA c.-29_-28delCT (0.52), embB p.Gln497Arg (0.73)
Pyrazinamide R pncA c.375_389delCGATGAGGTCGATGT (0.56)
Streptomycin R rrs n.517C>T (0.78)
Fluoroquinolones R gyrA p.Gly88Ala (0.43)
Moxifloxacin R gyrA p.Gly88Ala (0.43)
Ofloxacin R gyrA p.Gly88Ala (0.43)
Levofloxacin R gyrA p.Gly88Ala (0.43)
Ciprofloxacin R gyrA p.Gly88Ala (0.43)
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
lineage4 Euro-American LAM;T;S;X;H None 0.28
lineage1 Indo-Oceanic EAI RD239 0.68
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.29
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.74
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.23
lineage1.2.2.2 Indo-Oceanic NA RD239 0.73
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
gyrA 7564 p.Gly88Ala missense_variant 0.43 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Leu missense_variant 0.68 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.78 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.75 isoniazid
pncA 2288852 c.375_389delCGATGAGGTCGATGT disruptive_inframe_deletion 0.56 pyrazinamide
embA 4243203 c.-29_-28delCT upstream_gene_variant 0.52 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.73 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.85
gyrB 6112 p.Met291Ile missense_variant 0.67
gyrA 7268 c.-34C>T upstream_gene_variant 0.69
gyrA 7362 p.Glu21Gln missense_variant 0.97
gyrA 7585 p.Ser95Thr missense_variant 0.65
gyrA 8452 p.Ala384Val missense_variant 0.61
gyrA 9143 c.1842T>C synonymous_variant 0.64
gyrA 9304 p.Gly668Asp missense_variant 0.64
fgd1 491742 c.960T>C synonymous_variant 0.51
rpoC 763031 c.-339T>C upstream_gene_variant 0.55
rpoC 763552 c.183C>T synonymous_variant 0.78
rpoC 763884 p.Ala172Val missense_variant 0.7
rpoC 763886 c.517C>A synonymous_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 0.92
mmpL5 776100 p.Thr794Ile missense_variant 0.64
mmpR5 779121 c.138_139delTG frameshift_variant 0.5
mmpR5 779130 p.Asp47Glu missense_variant 0.53
mmpS5 779625 c.-720G>A upstream_gene_variant 0.64
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
embR 1417019 p.Cys110Tyr missense_variant 0.57
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 0.97
ndh 2102240 p.Arg268His missense_variant 0.45
katG 2154724 p.Arg463Leu missense_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 0.78
PPE35 2168149 p.Pro822Ser missense_variant 0.18
PPE35 2168742 p.Gly624Asp missense_variant 0.7
Rv1979c 2222098 p.Thr356Lys missense_variant 0.69
Rv1979c 2222308 p.Asp286Gly missense_variant 0.72
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.76
ahpC 2726051 c.-142G>A upstream_gene_variant 0.74
thyX 3068062 c.-117A>C upstream_gene_variant 0.6
ald 3086788 c.-32T>C upstream_gene_variant 0.73
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.67
fprA 3474597 c.591C>A synonymous_variant 0.64
fprA 3475159 p.Asn385Asp missense_variant 0.69
fbiB 3642874 p.Leu447Arg missense_variant 0.24
clpC1 4040517 p.Val63Ala missense_variant 0.68
clpC1 4040719 c.-15A>G upstream_gene_variant 0.77
embC 4240671 p.Thr270Ile missense_variant 0.74
embC 4241042 p.Asn394Asp missense_variant 0.68
embA 4242643 c.-590C>T upstream_gene_variant 0.96
embA 4245670 p.Ala813Gly missense_variant 0.64
embA 4245969 p.Pro913Ser missense_variant 0.9
embB 4246567 c.54_55insT frameshift_variant 0.35
embB 4246979 p.Gly156Cys missense_variant 0.71
embB 4247646 p.Glu378Ala missense_variant 0.76
aftB 4267960 p.Val293Met missense_variant 0.58
ubiA 4269387 p.Glu149Asp missense_variant 0.67
aftB 4269606 c.-770T>C upstream_gene_variant 0.65
ethA 4326148 c.1326G>T synonymous_variant 0.73
ethA 4326439 p.Asn345Lys missense_variant 0.72
whiB6 4338203 p.Arg107Cys missense_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.77
gid 4407588 c.615A>G synonymous_variant 0.84
gid 4407848 p.Ala119Thr missense_variant 0.71
gid 4407873 c.330G>T synonymous_variant 0.69