TB-Profiler result

Run: ERR2229607

Summary

Run ID: ERR2229607

Sample name:

Date: 31-03-2023 17:21:18

Number of reads: 919334

Percentage reads mapped: 99.22

Strain: lineage4.8

Drug-resistance: HR-TB


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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
katG 2155109 p.Ile335Val missense_variant 0.12 isoniazid
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
fgd1 491004 c.222G>T synonymous_variant 0.17
mshA 575484 p.Arg46Leu missense_variant 0.14
mshA 576524 p.His393Asn missense_variant 0.18
ccsA 620173 p.Val95Ile missense_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.2
mmpL5 775625 p.Trp952Cys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777307 p.Pro392Ser missense_variant 0.17
mmpL5 777637 p.Ile282Val missense_variant 0.11
mmpL5 777647 c.834C>G synonymous_variant 0.11
mmpL5 777877 p.Arg202Ser missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801103 p.Gln99* stop_gained 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304018 p.Asp363Gly missense_variant 0.2
Rv1258c 1407078 p.Gly88Ala missense_variant 0.11
embR 1416982 c.366C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475382 n.1725A>G non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
rpsA 1834418 p.Ile293Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917984 c.45C>A synonymous_variant 0.12
katG 2154640 p.Gly491Ala missense_variant 0.11
katG 2155313 p.Val267Ile missense_variant 0.14
PPE35 2168219 c.2394G>T synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169400 p.Gly405Cys missense_variant 0.15
PPE35 2169602 c.1011C>A synonymous_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.6
PPE35 2170392 p.Gly74Ala missense_variant 0.14
PPE35 2170400 c.213G>C synonymous_variant 0.14
Rv1979c 2222696 p.Arg157Trp missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517968 c.-147T>C upstream_gene_variant 0.17
kasA 2518271 p.Lys53* stop_gained 0.15
kasA 2518783 c.669T>C synonymous_variant 0.13
kasA 2518787 p.Arg225Trp missense_variant 0.13
kasA 2518790 p.Ala226Ser missense_variant 0.14
eis 2714850 c.483C>T synonymous_variant 0.13
folC 2747085 p.Val172Leu missense_variant 0.14
folC 2747290 c.309A>T synonymous_variant 0.13
pepQ 2860271 p.Arg50Ser missense_variant 0.12
ribD 2987306 c.468C>A synonymous_variant 0.14
Rv2752c 3064960 p.Ala411Val missense_variant 0.12
Rv2752c 3065111 p.Arg361Gly missense_variant 0.14
Rv2752c 3065687 p.Gly169Arg missense_variant 0.18
Rv2752c 3065742 c.450T>C synonymous_variant 0.15
Rv2752c 3067119 c.-928C>A upstream_gene_variant 0.11
fbiD 3339591 c.474G>T synonymous_variant 0.16
Rv3236c 3612588 p.Ser177Gly missense_variant 0.14
fbiB 3641867 c.333C>A synonymous_variant 0.14
alr 3840521 c.900C>A synonymous_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3877764 c.744C>A synonymous_variant 0.13
rpoA 3877850 p.Gly220Arg missense_variant 0.11
clpC1 4039730 c.975C>G synonymous_variant 0.14
embC 4240170 p.Thr103Lys missense_variant 0.12
embC 4241569 c.1707C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242922 c.-311C>A upstream_gene_variant 0.18
embA 4242967 c.-266C>A upstream_gene_variant 0.13
embA 4244895 p.Thr555Pro missense_variant 0.22
embA 4245795 p.Ala855Thr missense_variant 0.22
embB 4246103 c.-411C>T upstream_gene_variant 0.15
embB 4248052 c.1539G>T synonymous_variant 0.11
aftB 4268172 p.Val222Glu missense_variant 0.12
ubiA 4269906 c.-73G>T upstream_gene_variant 0.18
ethA 4326554 p.His307Arg missense_variant 0.11
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4327960 p.Trp138Arg missense_variant 0.17
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0