TB-Profiler result

Run: ERR6197037
Summary

Run ID: ERR6197037

Sample name:

Date: 02-04-2023 01:50:02

Number of reads: 2201238

Percentage reads mapped: 96.65

Strain: lineage4.3.4.2

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
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 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
rpoB 761155 p.Ser450Leu missense_variant 0.95 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.84 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.82 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288852 c.375_389delCGATGAGGTCGATGT disruptive_inframe_deletion 0.98 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.17
rpoC 764918 p.Val517Leu 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
Rv1258c 1406213 c.1128G>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.67
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.89
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.89
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.89
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.14
rrs 1473293 n.1448G>T non_coding_transcript_exon_variant 0.14
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.86
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.85
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.86
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.5
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.5
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.5
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.75
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.83
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.75
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.88
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.86
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.75
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.88
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.88
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 0.75
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.78
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.88
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.75
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.75
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.78
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.22
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.67
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.67
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.25
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.4
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.57
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.43
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.22
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.56
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.44
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.25
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.75
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.86
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.89
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 1.0
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 1.0
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 1.0
rpsA 1833469 c.-73G>T upstream_gene_variant 1.0
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 0.99
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 1.0
alr 3840719 c.702A>G synonymous_variant 0.96
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407970 p.Pro78Leu missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0