TB-Profiler result

Run: ERR2229397
Summary

Run ID: ERR2229397

Sample name:

Date: 31-03-2023 17:09:29

Number of reads: 632145

Percentage reads mapped: 98.84

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
gyrB 5439 p.Val67Ala missense_variant 0.18
gyrB 6225 p.Asn329Ser missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9341 c.2040C>G synonymous_variant 0.15
mshA 575169 c.-179A>C upstream_gene_variant 0.18
mshA 575308 c.-40A>T upstream_gene_variant 0.13
ccsA 619998 p.Phe36Leu missense_variant 0.25
ccsA 620062 p.Ser58Arg missense_variant 0.25
rpoB 760900 p.Asp365Ala missense_variant 0.18
rpoB 761007 p.Gln401Glu missense_variant 0.2
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 762397 p.Arg864Leu missense_variant 0.14
rpoC 764275 p.Phe302Leu missense_variant 0.29
rpoC 764912 p.Met515Leu missense_variant 0.14
rpoC 765792 p.Thr808Asn missense_variant 0.22
rpoC 766799 p.Ala1144Ser missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776080 p.Ala801Ser missense_variant 0.17
mmpL5 776081 c.2400G>A synonymous_variant 0.17
mmpL5 777164 c.1317C>T synonymous_variant 0.4
mmpS5 778757 p.Pro50Gln missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303980 c.1050G>T synonymous_variant 0.15
embR 1416677 p.Ala224Val missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472250 n.405G>C non_coding_transcript_exon_variant 0.17
rrl 1473864 n.207G>C non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476168 n.2511A>G non_coding_transcript_exon_variant 0.22
fabG1 1673357 c.-83G>A upstream_gene_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.39
rpsA 1833964 p.Asp141Glu missense_variant 0.14
rpsA 1834146 p.Phe202Ser missense_variant 0.15
rpsA 1834521 p.Ala327Val missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154906 c.1206G>A synonymous_variant 0.15
PPE35 2167812 p.Gln934Leu missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.21
PPE35 2169272 c.1341C>G synonymous_variant 0.21
PPE35 2169278 c.1335T>C synonymous_variant 0.29
PPE35 2169281 c.1332T>G synonymous_variant 0.27
PPE35 2169636 p.Ser326Ile missense_variant 0.17
PPE35 2169732 p.Asn294Ser missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.61
PPE35 2170553 c.59delG frameshift_variant 0.18
Rv1979c 2222268 c.897C>A synonymous_variant 0.25
Rv1979c 2222519 p.Gly216Arg missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518839 p.Ala242Gly missense_variant 0.4
eis 2715432 c.-100C>T upstream_gene_variant 0.12
eis 2715436 c.-104G>A upstream_gene_variant 0.12
eis 2715440 c.-108A>C upstream_gene_variant 0.12
eis 2715445 c.-113C>T upstream_gene_variant 0.13
eis 2715447 c.-115T>A upstream_gene_variant 0.12
eis 2715450 c.-118T>C upstream_gene_variant 0.14
eis 2715451 c.-119C>A upstream_gene_variant 0.14
eis 2715454 c.-122T>G upstream_gene_variant 0.14
eis 2715455 c.-123G>A upstream_gene_variant 0.14
eis 2715458 c.-126T>A upstream_gene_variant 0.14
eis 2715460 c.-128A>G upstream_gene_variant 0.14
eis 2715465 c.-133G>T upstream_gene_variant 0.15
eis 2715469 c.-137T>C upstream_gene_variant 0.15
eis 2715473 c.-141A>G upstream_gene_variant 0.15
pepQ 2859311 p.Ala370Ser missense_variant 0.2
pepQ 2859613 p.Glu269Gly missense_variant 0.18
pepQ 2860399 p.Arg7Gln missense_variant 0.13
pepQ 2860428 c.-10G>C upstream_gene_variant 0.11
Rv2752c 3064751 p.Arg481Ser missense_variant 0.18
thyA 3074495 c.-24C>T upstream_gene_variant 0.12
fbiD 3339463 p.Asp116Asn missense_variant 0.25
fprA 3474174 c.168T>C synonymous_variant 0.33
fprA 3474277 p.Gly91Cys missense_variant 0.25
whiB7 3568428 c.252A>G synonymous_variant 0.29
Rv3236c 3612334 p.Met261Ile missense_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.21
rpoA 3877592 c.916C>T synonymous_variant 0.2
rpoA 3877785 c.723C>A synonymous_variant 0.29
rpoA 3878188 p.Ala107Asp missense_variant 0.2
clpC1 4038883 p.Gly608Arg missense_variant 0.14
clpC1 4039017 p.Ser563Phe missense_variant 0.12
clpC1 4039631 c.1074C>A synonymous_variant 0.18
embC 4240276 c.414G>A synonymous_variant 0.15
embC 4240552 p.Lys230Asn missense_variant 0.12
embC 4241118 c.1257_1258insGGCAGC conservative_inframe_insertion 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244069 c.837C>A synonymous_variant 0.15
embA 4246420 p.Leu1063Pro missense_variant 0.17
embB 4246529 p.Ser6Arg missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.45
embB 4246548 p.Pro12Gln missense_variant 0.44
embB 4246554 p.Arg14Leu missense_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4249021 c.2508G>C synonymous_variant 0.1
aftB 4268573 p.Met88Ile missense_variant 0.2
ubiA 4269101 p.Gly245Arg missense_variant 0.15
ubiA 4270022 c.-189C>G upstream_gene_variant 0.14
ubiA 4270025 c.-192C>G upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0