TB-Profiler result

Run: ERR2503533
Summary

Run ID: ERR2503533

Sample name:

Date: 21-10-2023 16:18:09

Number of reads: 2309532

Percentage reads mapped: 96.67

Strain: lineage4.1.2.1

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.799C>T (0.45)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.45 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760106 c.300G>A synonymous_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_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 1471972 n.127T>C non_coding_transcript_exon_variant 0.15
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.27
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.34
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.32
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 0.28
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.31
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.31
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.33
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.35
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.34
rrs 1472278 n.433C>T non_coding_transcript_exon_variant 0.32
rrs 1472279 n.434T>C non_coding_transcript_exon_variant 0.32
rrs 1472297 n.454_457delTCCG non_coding_transcript_exon_variant 0.24
rrs 1472304 n.459G>T non_coding_transcript_exon_variant 0.24
rrs 1472307 n.464_471delCTCGGATT non_coding_transcript_exon_variant 0.27
rrs 1472325 n.480G>A non_coding_transcript_exon_variant 0.28
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.31
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.28
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.28
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.28
rrs 1472447 n.602C>T non_coding_transcript_exon_variant 0.23
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.23
rrs 1472450 n.605A>G non_coding_transcript_exon_variant 0.23
rrs 1472451 n.606C>G non_coding_transcript_exon_variant 0.23
rrs 1472461 n.616G>C non_coding_transcript_exon_variant 0.24
rrs 1472462 n.617T>C non_coding_transcript_exon_variant 0.25
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.27
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.32
rrs 1472485 n.640delGinsTA non_coding_transcript_exon_variant 0.35
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.38
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.44
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.43
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.46
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.31
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.33
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.31
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.31
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.35
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.35
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.36
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.32
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.34
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.34
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.33
rrs 1472993 n.1148G>A non_coding_transcript_exon_variant 0.33
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.44
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.24
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.38
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.35
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.33
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.24
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.24
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.5
rrl 1474798 n.1141C>G non_coding_transcript_exon_variant 0.54
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.53
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.53
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.53
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.53
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.51
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.44
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.31
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.26
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.26
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.18
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.19
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.27
rrl 1475769 n.2112_2113insC non_coding_transcript_exon_variant 0.28
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.48
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.48
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.48
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.48
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.31
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.52
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.55
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.51
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.5
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.51
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.51
rrl 1476029 n.2372A>T non_coding_transcript_exon_variant 0.49
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.5
rrl 1476035 n.2378G>A non_coding_transcript_exon_variant 0.53
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.51
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.49
rrl 1476091 n.2434_2435insC non_coding_transcript_exon_variant 0.45
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.43
rrl 1476100 n.2443A>C non_coding_transcript_exon_variant 0.43
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.43
rrl 1476105 n.2450delA non_coding_transcript_exon_variant 0.43
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.43
rrl 1476113 n.2456T>G non_coding_transcript_exon_variant 0.42
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.43
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.33
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.36
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.38
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.4
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.36
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.36
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.29
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.31
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.32
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.29
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.32
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.32
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.28
rrl 1476269 n.2612C>G non_coding_transcript_exon_variant 0.29
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476523 n.2867delC non_coding_transcript_exon_variant 0.27
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.3
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.3
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.99
embA 4245476 c.2244C>T synonymous_variant 1.0
aftB 4268016 p.Val274Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407605 p.Ala200Thr missense_variant 1.0