TB-Profiler result

Run: ERR176565
Summary

Run ID: ERR176565

Sample name:

Date: 24-01-2024 12:25:07

Number of reads: 2633132

Percentage reads mapped: 88.21

Strain: lineage4.3.4.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.4 Euro-American (LAM) LAM RD174 0.98
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.98
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.99
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
gyrB 6140 p.Val301Leu missense_variant 0.96
gyrA 6445 c.-857C>T upstream_gene_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.97
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.39
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.39
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.35
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.33
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.3
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.19
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.16
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.25
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.25
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.26
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.19
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.25
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.18
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.18
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.18
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.18
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.18
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.17
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.17
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.17
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.17
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.17
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.19
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.22
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.22
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.28
rrs 1473194 n.1349A>G non_coding_transcript_exon_variant 0.29
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.16
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.16
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.15
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrs 1473262 n.1417T>A non_coding_transcript_exon_variant 0.14
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.17
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.17
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.17
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.18
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.2
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.24
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.23
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.26
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.33
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.33
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.37
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.34
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.38
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.43
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.46
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.51
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.45
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.42
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.39
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.95
alr 3840719 c.702A>G synonymous_variant 0.97
clpC1 4038287 c.2418C>T synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247126 p.Thr205Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0