TB-Profiler result

Run: ERR4797089
Summary

Run ID: ERR4797089

Sample name:

Date: 20-10-2023 02:13:12

Number of reads: 5907984

Percentage reads mapped: 99.52

Strain: lineage4.3.3;lineage1.1.3.1

Drug-resistance: Pre-XDR-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.Ser450Leu (0.41)
Isoniazid R katG p.Ser315Thr (0.27)
Ethambutol R embB p.Met306Val (0.36)
Pyrazinamide R pncA p.Ala171Val (0.45)
Streptomycin R rpsL p.Lys43Arg (0.27)
Fluoroquinolones R gyrA p.Ala90Val (0.35)
Moxifloxacin R gyrA p.Ala90Val (0.35)
Ofloxacin R gyrA p.Ala90Val (0.35)
Levofloxacin R gyrA p.Ala90Val (0.35)
Ciprofloxacin R gyrA p.Ala90Val (0.35)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.223_226dupATCG (0.18), ethA c.223_226dupATCG (0.18)
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 0.3
lineage1 Indo-Oceanic EAI RD239 0.65
lineage4.3 Euro-American (LAM) mainly-LAM None 0.31
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.64
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.68
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.33
lineage1.1.3.1 Indo-Oceanic NA RD239 0.66
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 7570 p.Ala90Val missense_variant 0.35 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.41 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.27 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.27 isoniazid
pncA 2288730 p.Ala171Val missense_variant 0.45 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.36 ethambutol
ethA 4327247 c.223_226dupATCG frameshift_variant 0.18 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 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.33
gyrA 8452 p.Ala384Val missense_variant 0.63
gyrA 9143 c.1842T>C synonymous_variant 0.69
gyrA 9276 p.Leu659Val missense_variant 0.72
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.66
rpoC 762929 c.-441G>A upstream_gene_variant 0.66
rpoC 763031 c.-339T>C upstream_gene_variant 0.66
rpoC 763884 p.Ala172Val missense_variant 0.68
rpoC 763886 c.517C>A synonymous_variant 0.68
rpoC 764995 c.1626C>G synonymous_variant 0.33
rpoC 765171 p.Pro601Leu missense_variant 0.54
rpoC 765230 p.Ala621Thr missense_variant 0.56
rpoC 766487 p.Pro1040Thr missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.76
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474301 n.644G>A non_coding_transcript_exon_variant 0.57
rpsA 1834836 p.Met432Thr missense_variant 0.37
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153940 c.2172C>T synonymous_variant 0.77
katG 2154724 p.Arg463Leu missense_variant 0.68
katG 2156196 c.-85C>T upstream_gene_variant 0.32
PPE35 2167926 p.Leu896Ser missense_variant 0.74
PPE35 2167983 p.Gly877Asp missense_variant 0.76
Rv1979c 2222308 p.Asp286Gly missense_variant 0.8
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289351 c.-110C>A upstream_gene_variant 0.63
kasA 2518132 c.18C>T synonymous_variant 0.72
kasA 2518919 p.Gly269Ser missense_variant 0.35
ahpC 2726051 c.-142G>A upstream_gene_variant 0.71
folC 2746340 p.Ala420Val missense_variant 0.37
Rv2752c 3064632 c.1560C>T synonymous_variant 0.73
thyA 3073868 p.Thr202Ala missense_variant 0.34
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.73
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.72
fprA 3475159 p.Asn385Asp missense_variant 0.59
alr 3841253 c.168C>T synonymous_variant 0.65
clpC1 4038287 c.2418C>T synonymous_variant 0.26
clpC1 4040517 p.Val63Ala missense_variant 0.8
embC 4240671 p.Thr270Ile missense_variant 0.5
embC 4241042 p.Asn394Asp missense_variant 0.59
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.56
embA 4244099 c.867T>C synonymous_variant 0.62
embA 4245969 p.Pro913Ser missense_variant 0.64
embB 4247646 p.Glu378Ala missense_variant 0.78
ubiA 4269387 p.Glu149Asp missense_variant 0.74
ubiA 4269391 p.Val148Ala missense_variant 0.27
aftB 4269606 c.-770T>C upstream_gene_variant 0.73
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407780 c.423G>A synonymous_variant 0.8
gid 4407806 p.Ala133Thr missense_variant 0.27
gid 4407873 c.330G>T synonymous_variant 0.64
gid 4408156 p.Leu16Arg missense_variant 0.31