TB-Profiler result

Run: SRR2100184
Summary

Run ID: SRR2100184

Sample name:

Date: 19-10-2023 15:36:37

Number of reads: 4697401

Percentage reads mapped: 99.38

Strain: lineage4.1.1.3;lineage1.1.2

Drug-resistance: RR-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.Asp435Tyr (0.26)
Isoniazid
Ethambutol
Pyrazinamide R panD p.Ile49Val (0.84)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
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
lineage1 Indo-Oceanic EAI RD239 0.8
lineage4.1 Euro-American T;X;H None 0.25
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.76
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.78
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.22
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.19
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 761109 p.Asp435Tyr missense_variant 0.26 rifampicin
panD 4044137 p.Ile49Val missense_variant 0.84 pyrazinamide
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 5770 c.531C>T synonymous_variant 0.8
gyrB 6112 p.Met291Ile missense_variant 0.79
gyrB 6124 c.885C>T synonymous_variant 0.77
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.74
gyrA 9143 c.1842T>C synonymous_variant 0.79
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.78
rpoC 763031 c.-339T>C upstream_gene_variant 0.75
rpoC 763884 p.Ala172Val missense_variant 0.74
rpoC 763886 c.517C>A synonymous_variant 0.73
rpoC 765150 p.Gly594Glu missense_variant 0.22
rpoC 765171 p.Pro601Leu missense_variant 0.77
rpoC 765190 c.1821G>A synonymous_variant 0.76
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpR5 779434 p.Val149Ile missense_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406503 p.Val280Leu missense_variant 0.79
embR 1417019 p.Cys110Tyr missense_variant 0.69
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.79
PPE35 2167926 p.Leu896Ser missense_variant 0.8
PPE35 2167983 p.Gly877Asp missense_variant 0.83
Rv1979c 2222308 p.Asp286Gly missense_variant 0.76
Rv1979c 2223170 c.-6G>A upstream_gene_variant 0.23
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
ribD 2987151 p.His105Tyr missense_variant 0.75
Rv2752c 3064632 c.1560C>T synonymous_variant 0.68
Rv2752c 3065598 c.594G>A synonymous_variant 0.66
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 0.71
fprA 3475159 p.Asn385Asp missense_variant 0.78
rpoA 3878569 c.-63_-62insG upstream_gene_variant 0.82
clpC1 4040517 p.Val63Ala missense_variant 0.72
embC 4240671 p.Thr270Ile missense_variant 0.82
embC 4241042 p.Asn394Asp missense_variant 0.74
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.18
embA 4243848 p.Val206Met missense_variant 0.74
embA 4245969 p.Pro913Ser missense_variant 0.85
embB 4247646 p.Glu378Ala missense_variant 0.76
embB 4249408 c.2895G>A synonymous_variant 0.25
aftB 4267867 p.Leu324Met missense_variant 0.77
aftB 4268461 p.Ile126Val missense_variant 0.8
ubiA 4269387 p.Glu149Asp missense_variant 0.76
aftB 4269606 c.-770T>C upstream_gene_variant 0.78
aftB 4269630 c.-794G>A upstream_gene_variant 0.71
whiB6 4338596 c.-76_-75delAGinsC upstream_gene_variant 0.73
whiB6 4338596 c.-75delG upstream_gene_variant 0.27
whiB6 4338603 c.-82C>T upstream_gene_variant 0.75
gid 4407588 c.615A>G synonymous_variant 0.8
gid 4407798 c.405G>T synonymous_variant 0.29
gid 4407873 c.330G>T synonymous_variant 0.71