TB-Profiler result

Run: ERR2229707

Summary

Run ID: ERR2229707

Sample name:

Date: 31-03-2023 17:27:57

Number of reads: 599364

Percentage reads mapped: 99.31

Strain: lineage4.8

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
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 8831 c.1530G>A synonymous_variant 0.14
fgd1 491281 p.Asp167Asn missense_variant 0.25
ccsA 620811 c.921G>A synonymous_variant 0.13
rpoB 759721 c.-86G>C upstream_gene_variant 0.13
rpoB 760690 p.Phe295Ser missense_variant 0.11
rpoB 762433 p.Gly876Asp missense_variant 0.12
rpoC 765181 c.1812G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776080 p.Ala801Ser missense_variant 0.25
mmpL5 776081 c.2400G>A synonymous_variant 0.17
mmpL5 776087 c.2394C>G synonymous_variant 0.15
mmpL5 776093 c.2386_2388delCGCinsAGA synonymous_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 0.13
mmpL5 776103 p.Ile793Gly missense_variant 0.14
mmpL5 776105 c.2376G>C synonymous_variant 0.14
mmpL5 777081 p.Lys467Met missense_variant 0.14
mmpL5 777625 p.Gln286Lys missense_variant 0.12
mmpS5 779527 c.-622C>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781642 p.Pro28Gln missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406409 p.Leu311Pro missense_variant 0.29
embR 1417156 c.191delC frameshift_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
inhA 1674346 p.Arg49Cys missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102293 c.750C>T synonymous_variant 0.14
ndh 2103177 c.-135G>T upstream_gene_variant 0.14
katG 2154369 c.1743G>A synonymous_variant 0.14
katG 2154918 c.1194G>A synonymous_variant 0.14
katG 2156228 c.-117T>C upstream_gene_variant 0.13
katG 2156398 c.-287C>A upstream_gene_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.11
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2169287 c.1326T>C synonymous_variant 0.12
PPE35 2169293 c.1320T>C synonymous_variant 0.11
PPE35 2169308 c.1305C>T synonymous_variant 0.11
PPE35 2169457 p.His386Asp missense_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.48
PPE35 2170053 p.Thr187Ser missense_variant 0.48
PPE35 2170379 c.234G>T synonymous_variant 0.11
PPE35 2170382 c.231C>T synonymous_variant 0.11
PPE35 2170469 c.144G>C synonymous_variant 0.1
Rv1979c 2222870 p.Ala99Thr missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518652 p.His180Asn missense_variant 0.17
Rv2752c 3064737 p.Gln485His missense_variant 0.29
thyX 3067431 p.Arg172Pro missense_variant 0.17
thyX 3067607 p.Asp113Glu missense_variant 0.15
thyA 3074173 p.Ser100Leu missense_variant 0.12
thyA 3074544 c.-73T>G upstream_gene_variant 0.22
Rv3083 3448386 c.-118C>T upstream_gene_variant 0.14
fbiB 3641493 c.-42T>G upstream_gene_variant 0.12
fbiB 3642328 p.Arg265Gln missense_variant 0.12
rpoA 3878087 p.Glu141Gln missense_variant 0.12
clpC1 4038752 p.Gln651His missense_variant 0.15
clpC1 4038773 p.Asp644Glu missense_variant 0.17
clpC1 4038776 p.Glu643Asp missense_variant 0.17
clpC1 4040271 p.Tyr145Phe missense_variant 0.2
embC 4239878 c.20delC frameshift_variant 0.18
embC 4241063 p.Ile401Val missense_variant 0.18
embC 4241097 p.Ser412* stop_gained 0.15
embC 4241461 c.1599C>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.33
embA 4244519 c.1287G>C synonymous_variant 0.18
embA 4244534 c.1304delG frameshift_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.19
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.57
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4246563 p.Leu17Trp missense_variant 0.38
embB 4246567 c.54G>T synonymous_variant 0.31
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4247564 p.Arg351Gly missense_variant 0.18
embB 4249035 p.Arg841Gln missense_variant 0.33
embB 4249285 p.Glu924Asp missense_variant 0.14
aftB 4268189 c.648C>A synonymous_variant 0.14
aftB 4268510 p.Ser109Arg missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408281 c.-79C>T upstream_gene_variant 0.13
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0