TB-Profiler result

Run: ERR2229581
Summary

Run ID: ERR2229581

Sample name:

Date: 31-03-2023 17:20:04

Number of reads: 453067

Percentage reads mapped: 95.36

Strain: lineage4.8

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
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
ethA 4326048 p.Glu476* stop_gained 0.13 ethionamide
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 7874 c.573G>A synonymous_variant 0.13
gyrA 8359 p.Pro353Gln missense_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.4
mshA 576439 c.1092G>T synonymous_variant 0.29
mshA 576741 p.Ala465Glu missense_variant 0.18
rpoC 764075 p.Val236Ile missense_variant 0.18
mmpL5 776905 p.Val526Phe missense_variant 0.33
mmpL5 777164 c.1317C>T synonymous_variant 0.18
mmpL5 777173 c.1308C>T synonymous_variant 0.18
mmpL5 777176 p.Glu435Asp missense_variant 0.2
mmpL5 777198 p.Asn428Ile missense_variant 0.2
mmpS5 778759 p.Glu49Asp missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781924 p.Glu122Val missense_variant 0.12
fbiC 1303624 p.Gly232Cys missense_variant 0.67
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304701 c.1774delC frameshift_variant 0.14
embR 1417444 c.-97T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.25
rrl 1473977 n.320G>A non_coding_transcript_exon_variant 1.0
rrl 1474112 n.455T>A non_coding_transcript_exon_variant 0.4
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34
inhA 1674957 c.756G>C synonymous_variant 0.25
rpsA 1833487 c.-55C>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>A upstream_gene_variant 0.14
katG 2156497 c.-386T>G upstream_gene_variant 0.5
PPE35 2167738 p.Leu959Met missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169472 p.Ser381Cys missense_variant 0.14
PPE35 2169488 c.1125G>C synonymous_variant 0.18
PPE35 2169491 c.1122T>C synonymous_variant 0.18
PPE35 2169581 c.1032C>G synonymous_variant 0.29
PPE35 2169587 c.1026G>A synonymous_variant 0.4
PPE35 2169902 c.711G>C synonymous_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.42
PPE35 2170308 p.Leu102Ala missense_variant 0.14
PPE35 2170313 c.300G>C synonymous_variant 0.14
Rv1979c 2222037 c.1128C>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518241 p.Ile43Leu missense_variant 0.2
kasA 2519311 p.Asn399Lys missense_variant 0.25
eis 2714401 p.Ala311Asp missense_variant 0.25
eis 2715272 p.Ala21Pro missense_variant 0.13
ahpC 2725993 c.-200A>G upstream_gene_variant 0.12
ahpC 2726373 p.Cys61Ser missense_variant 0.15
ahpC 2726644 p.Ala151Gly missense_variant 0.29
folC 2746616 p.Ala328Asp missense_variant 0.4
pepQ 2859405 c.1014C>T synonymous_variant 0.2
pepQ 2859487 p.Thr311Lys missense_variant 0.22
pepQ 2859585 c.834C>A synonymous_variant 0.29
pepQ 2859973 p.Ala149Gly missense_variant 0.29
Rv2752c 3065274 c.918C>A synonymous_variant 0.22
Rv2752c 3066125 p.Gly23Ser missense_variant 0.33
thyX 3067789 p.Lys53* stop_gained 0.2
fprA 3474779 p.Arg258Leu missense_variant 0.4
whiB7 3568428 c.252A>G synonymous_variant 0.5
fbiA 3640659 p.His39Gln missense_variant 0.12
fbiB 3642172 p.Pro213Arg missense_variant 0.33
fbiB 3642241 p.Gly236Asp missense_variant 0.33
alr 3840601 p.Ala274Ser missense_variant 0.12
alr 3840728 c.693G>A synonymous_variant 0.22
alr 3841539 c.-119C>T upstream_gene_variant 0.44
alr 3841546 c.-126C>A upstream_gene_variant 0.62
rpoA 3878358 c.150C>T synonymous_variant 0.25
clpC1 4038332 c.2373C>T synonymous_variant 0.22
clpC1 4040144 c.561G>T synonymous_variant 0.22
panD 4044190 p.Asp31Val missense_variant 0.22
panD 4044443 c.-162G>A upstream_gene_variant 0.13
embC 4241436 p.Ala525Val missense_variant 0.33
embC 4242306 p.Ile815Asn missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243534 p.Gly101Asp missense_variant 0.33
embA 4243925 c.693C>A synonymous_variant 0.14
embA 4244214 p.Ala328Ser missense_variant 0.22
embA 4244998 p.Ala589Val missense_variant 0.18
embA 4245415 p.Thr728Ser missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 1.0
embB 4247314 c.801G>A synonymous_variant 0.15
embB 4247322 p.Pro270Gln missense_variant 0.17
embB 4248562 c.2049G>T synonymous_variant 0.18
aftB 4267280 p.Glu519Asp missense_variant 0.2
ethA 4326401 p.Gly358Val missense_variant 0.2
ethA 4326529 p.Asp315Glu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338645 c.-124G>T upstream_gene_variant 0.12
gid 4408218 c.-16G>T upstream_gene_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0