TB-Profiler result

Run: ERR6197043
Summary

Run ID: ERR6197043

Sample name:

Date: 02-04-2023 01:50:18

Number of reads: 2391620

Percentage reads mapped: 95.35

Strain: lineage4.3.4.2

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;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
rpoB 761127 p.Ser441Ala missense_variant 0.1 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.95 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.63 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.71 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288852 c.375_389delCGATGAGGTCGATGT disruptive_inframe_deletion 0.99 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.98 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 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
rpoB 761051 c.1245G>C synonymous_variant 0.13
rpoB 761054 c.1248G>C synonymous_variant 0.17
rpoB 761057 c.1251G>C synonymous_variant 0.12
rpoB 761060 c.1254C>G synonymous_variant 0.17
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.13
rpoB 761096 c.1290G>C synonymous_variant 0.1
rpoB 761102 c.1296A>G synonymous_variant 0.11
rpoC 762989 c.-381G>C upstream_gene_variant 0.13
rpoB 763005 p.Cys1067Gly missense_variant 0.11
rpoC 763028 c.-342T>C upstream_gene_variant 0.12
rpoC 763053 c.-317T>C upstream_gene_variant 0.11
rpoC 764605 c.1236G>T synonymous_variant 0.11
rpoC 764611 c.1242G>T synonymous_variant 0.12
rpoC 764632 c.1263T>C synonymous_variant 0.1
rpoC 764918 p.Val517Leu missense_variant 0.98
rpoC 764995 c.1626C>G synonymous_variant 0.98
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 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0
rrs 1472351 n.506G>T non_coding_transcript_exon_variant 1.0
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 1.0
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 1.0
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 1.0
rrs 1472461 n.616G>C non_coding_transcript_exon_variant 1.0
rrs 1472462 n.617T>C non_coding_transcript_exon_variant 1.0
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 1.0
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 1.0
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 1.0
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 1.0
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 1.0
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.67
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.67
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.4
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.4
rrs 1472664 n.819A>G non_coding_transcript_exon_variant 0.5
rrs 1472666 n.821G>A non_coding_transcript_exon_variant 0.5
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.5
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.5
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.5
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.4
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.4
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.4
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.4
rrs 1472694 n.849C>T non_coding_transcript_exon_variant 0.4
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.4
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.67
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.67
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 1.0
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.8
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.83
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.83
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.78
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.8
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.7
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.9
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.8
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.9
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.9
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.9
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.73
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.92
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.18
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.15
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.76
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.12
rrs 1473158 n.1313T>C non_coding_transcript_exon_variant 0.12
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.72
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.13
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.24
rrs 1473177 n.1332G>T non_coding_transcript_exon_variant 0.12
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrs 1473193 n.1348G>C non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.71
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.91
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.64
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.67
rrs 1473287 n.1442_1443delCC non_coding_transcript_exon_variant 0.7
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.23
rrs 1473293 n.1448G>T non_coding_transcript_exon_variant 0.23
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.72
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.7
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.76
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 1.0
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 1.0
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 1.0
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 1.0
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 1.0
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 1.0
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.95
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.95
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.13
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.11
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.14
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.24
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.11
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.16
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
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
rpsA 1834249 c.708T>C synonymous_variant 0.1
rpsA 1834261 c.720A>G synonymous_variant 0.1
rpsA 1834298 p.Gln253Glu missense_variant 0.11
rpsA 1834306 c.765T>C synonymous_variant 0.12
rpsA 1834312 c.771G>A synonymous_variant 0.11
rpsA 1834327 c.786G>T synonymous_variant 0.12
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 0.99
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243999 p.Ala256Val missense_variant 0.11
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