TB-Profiler result

Run: ERR2513140
Summary

Run ID: ERR2513140

Sample name:

Date: 31-03-2023 19:29:08

Number of reads: 648947

Percentage reads mapped: 99.7

Strain: lineage4.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7794 p.Val165Met missense_variant 0.1
gyrA 8362 p.Arg354Leu missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9782 c.2481C>T synonymous_variant 0.17
fgd1 490714 c.-69G>C upstream_gene_variant 0.11
fgd1 490751 c.-32T>G upstream_gene_variant 0.25
mshA 575777 p.Glu144Lys missense_variant 0.11
rpoB 759900 c.94C>A synonymous_variant 0.11
rpoC 764572 c.1203G>C synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765725 p.Gly786Ser missense_variant 0.18
rpoC 765844 c.2475C>A synonymous_variant 0.11
rpoC 766633 c.3264G>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777662 c.819C>G synonymous_variant 0.12
mmpR5 779158 p.Ala57Thr missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303678 p.Arg250Trp missense_variant 0.14
fbiC 1303833 c.903C>G synonymous_variant 0.1
Rv1258c 1407055 c.285delG frameshift_variant 0.2
embR 1416222 p.Phe376Leu missense_variant 0.11
embR 1416232 p.Cys372Gly missense_variant 0.12
embR 1416259 c.1089G>C synonymous_variant 0.12
embR 1416262 c.1086G>C synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475430 n.1773T>C non_coding_transcript_exon_variant 0.67
inhA 1673904 c.-298C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154849 c.1263T>A synonymous_variant 0.12
PPE35 2170066 p.Ala183Thr missense_variant 0.29
Rv1979c 2222715 c.450C>T synonymous_variant 0.12
Rv1979c 2222956 p.Arg70Lys missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290220 c.-979G>A upstream_gene_variant 0.12
eis 2714283 c.1050A>G synonymous_variant 0.12
eis 2714919 c.414T>C synonymous_variant 0.2
ahpC 2726338 p.Val49Gly missense_variant 0.18
folC 2746471 c.1128C>T synonymous_variant 0.18
pepQ 2860375 p.Ala15Asp missense_variant 0.11
Rv2752c 3065983 p.Arg70Gln missense_variant 0.14
Rv2752c 3067099 c.-908C>T upstream_gene_variant 0.12
Rv2752c 3067144 c.-953G>A upstream_gene_variant 0.25
thyX 3067729 c.217C>T synonymous_variant 0.14
thyA 3073707 c.765G>A synonymous_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087118 p.Ser100* stop_gained 0.15
ald 3087285 p.Arg156Cys missense_variant 0.12
Rv3083 3449334 c.831C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613032 p.Ala29Thr missense_variant 0.22
fbiA 3641143 p.Ala201Ser missense_variant 0.15
fbiB 3641487 c.-48G>A upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240468 c.606C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245762 p.Gly844Trp missense_variant 0.13
embB 4247426 p.Gly305Thr missense_variant 0.12
ubiA 4269864 c.-31C>G upstream_gene_variant 0.25
ethA 4327188 p.Arg96Gly missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0