TB-Profiler result

Run: SRR6045547
Summary

Run ID: SRR6045547

Sample name:

Date: 20-10-2023 18:17:54

Number of reads: 3366534

Percentage reads mapped: 97.07

Strain: lineage4.9;lineage3.1.2

Drug-resistance: Sensitive

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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
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
lineage3 East-African-Indian CAS RD750 0.44
lineage4 Euro-American LAM;T;S;X;H None 0.59
lineage4.9 Euro-American (H37Rv-like) T1 None 0.66
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.4
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.43
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
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
gyrA 7362 p.Glu21Gln missense_variant 0.39
gyrA 7585 p.Ser95Thr missense_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 0.31
fgd1 491742 c.960T>C synonymous_variant 0.31
rpoB 759746 c.-61C>T upstream_gene_variant 0.32
rpoC 762434 c.-936T>G upstream_gene_variant 0.39
rpoC 763031 c.-339T>C upstream_gene_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 0.39
mmpL5 776100 p.Thr794Ile missense_variant 0.32
rpsL 781395 c.-165T>C upstream_gene_variant 0.46
rrs 1471659 n.-187C>T upstream_gene_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.12
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.33
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.28
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.29
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.26
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.26
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.26
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.26
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.26
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.25
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.25
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.25
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.26
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.24
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.29
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.39
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.3
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.3
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.3
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.26
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 0.29
tlyA 1918696 p.Ala253Pro missense_variant 0.44
katG 2154724 p.Arg463Leu missense_variant 0.43
PPE35 2167926 p.Leu896Ser missense_variant 0.32
PPE35 2168604 p.Pro670Leu missense_variant 0.41
Rv1979c 2223257 c.-93G>C upstream_gene_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.28
pncA 2289047 c.195C>T synonymous_variant 0.46
pncA 2289365 c.-125delC upstream_gene_variant 0.43
eis 2715432 c.-100C>T upstream_gene_variant 0.37
ahpC 2726105 c.-88G>A upstream_gene_variant 0.45
ald 3086788 c.-32T>C upstream_gene_variant 0.39
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.38
fprA 3475052 p.Asn349Thr missense_variant 0.46
embC 4242075 p.Arg738Gln missense_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 0.55
embB 4248241 c.1728C>G synonymous_variant 0.4
ethR 4327693 p.Asp49Asn missense_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 0.45
gid 4407588 c.615A>G synonymous_variant 0.34
gid 4408147 p.Ala19Val missense_variant 0.34