TB-Profiler result

Run: ERR181761

Summary

Run ID: ERR181761

Sample name:

Date: 24-01-2024 12:25:35

Number of reads: 3659079

Percentage reads mapped: 87.11

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 0.96
lineage4.3.4 Euro-American (LAM) LAM RD174 0.98
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.97
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.98
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 0.94
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.97
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 1472129 n.284G>C non_coding_transcript_exon_variant 0.1
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.12
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.11
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.13
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.12
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.14
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.18
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.21
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.21
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.21
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.13
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.14
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.14
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.14
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.13
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.13
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.13
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.24
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.26
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.3
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.31
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.34
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.43
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.21
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.12
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.12
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.12
rrl 1476624 n.2967T>G non_coding_transcript_exon_variant 0.12
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.11
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.1
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 1.0
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 0.96
alr 3840719 c.702A>G synonymous_variant 0.94
clpC1 4038287 c.2418C>T synonymous_variant 0.95
embC 4241539 c.1677T>C synonymous_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.97