TB-Profiler result

Run: ERR2229532
Summary

Run ID: ERR2229532

Sample name:

Date: 31-03-2023 17:17:19

Number of reads: 846718

Percentage reads mapped: 99.4

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 4326419 c.1054delG frameshift_variant 0.12 ethionamide, ethionamide
ethA 4326525 c.948delC frameshift_variant 0.12 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
gyrB 6190 p.Glu317Asp missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 766272 p.Cys968Phe missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776181 p.Asp767Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Ala missense_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474095 n.438A>G non_coding_transcript_exon_variant 0.11
rrl 1475958 n.2301C>A non_coding_transcript_exon_variant 0.18
rrl 1476364 n.2707A>T non_coding_transcript_exon_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
fabG1 1674131 p.Tyr231Phe missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.46
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289126 p.Ala39Glu missense_variant 0.14
pncA 2289422 c.-181C>G upstream_gene_variant 0.1
eis 2714720 p.Lys205Glu missense_variant 0.11
eis 2715057 c.276C>A synonymous_variant 0.11
folC 2746317 p.Asp428Tyr missense_variant 0.18
folC 2746737 p.Asp288Asn missense_variant 0.17
folC 2746783 c.816C>T synonymous_variant 0.22
pepQ 2860103 p.Gly106Arg missense_variant 0.18
pepQ 2860147 p.Gly91Asp missense_variant 0.14
pepQ 2860339 p.Leu27Gln missense_variant 0.17
Rv2752c 3066130 p.Leu21Pro missense_variant 0.12
Rv2752c 3067176 c.-985A>C upstream_gene_variant 0.13
thyA 3074579 c.-108G>A upstream_gene_variant 0.13
thyA 3074580 c.-109T>C upstream_gene_variant 0.13
fbiD 3339531 p.Ser138Arg missense_variant 0.15
fbiD 3339542 p.Asp142Val missense_variant 0.14
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
clpC1 4040144 c.561G>C synonymous_variant 0.25
clpC1 4040149 p.Lys186Glu missense_variant 0.12
clpC1 4040241 p.Thr155Phe missense_variant 0.14
clpC1 4040249 p.Glu152Gly missense_variant 0.15
panD 4044028 p.Val85Ala missense_variant 0.13
panD 4044113 p.Thr57Ser missense_variant 0.22
embC 4242257 p.Val799Met missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245774 p.Leu848Met missense_variant 0.14
embB 4247968 c.1455C>A synonymous_variant 0.13
embB 4249203 p.Thr897Ile missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0