TB-Profiler result

Run: ERR4821958
Summary

Run ID: ERR4821958

Sample name:

Date: 20-10-2023 09:46:37

Number of reads: 4241042

Percentage reads mapped: 93.82

Strain: lineage4.3.3

Drug-resistance: Other

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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 R rrs n.888G>A (0.42)
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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 1.0
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.42 streptomycin
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 7058 p.Ile607Val missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
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
fbiC 1303095 c.165G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.5
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.63
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.63
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.52
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.74
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.68
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.77
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.84
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.89
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.59
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.53
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.56
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.64
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.62
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.63
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.23
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.66
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.67
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.63
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.26
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.65
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.26
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.6
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.6
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.6
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.37
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.3
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.42
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.41
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.42
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.47
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.38
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.29
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.78
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.78
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.85
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.82
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.58
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.56
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.67
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.73
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.78
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.78
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.81
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.79
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.79
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.78
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.82
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.74
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.75
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.69
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.62
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.62
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.51
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.62
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.71
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.64
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.64
rrs 1473288 n.1443_1444delCTinsGCTTTTG non_coding_transcript_exon_variant 0.56
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.59
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.59
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.59
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.56
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.89
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.89
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.94
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.94
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.94
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.59
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.68
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.79
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.8
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.48
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_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
fbiB 3642743 c.1209T>C synonymous_variant 0.3
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268566 p.Ser91Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0