TB-Profiler result

Run: ERR7801247

Summary

Run ID: ERR7801247

Sample name:

Date: 02-04-2023 06:00:17

Number of reads: 453676

Percentage reads mapped: 99.48

Strain: lineage4.3.4.2

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575918 p.Gly191Ser missense_variant 0.18
mshA 576434 p.Gln363Lys missense_variant 0.14
rpoB 762497 p.Asp897Glu missense_variant 0.15
rpoB 762769 p.Pro988His missense_variant 0.14
rpoC 763052 c.-318G>T upstream_gene_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766075 c.2706C>A synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777263 c.1218G>T synonymous_variant 0.2
mmpL5 777286 p.Ala399Ser missense_variant 0.15
mmpL5 777357 p.Arg375Leu missense_variant 0.18
mmpL5 778747 c.-267C>A upstream_gene_variant 0.22
mmpR5 779186 p.Gly66Val missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303554 c.624G>A synonymous_variant 0.14
fbiC 1303983 c.1053C>A synonymous_variant 0.15
Rv1258c 1406831 c.510C>A synonymous_variant 0.17
embR 1417209 p.Asn47Tyr missense_variant 0.15
embR 1417262 p.Pro29Gln missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833988 c.447C>T synonymous_variant 0.2
rpsA 1834132 p.Glu197Asp missense_variant 0.17
tlyA 1917751 c.-189A>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102141 p.Gly301Asp missense_variant 0.14
katG 2154227 p.Gly629Cys missense_variant 0.18
katG 2155583 p.Gly177Cys missense_variant 0.22
katG 2155641 p.Lys157Asn missense_variant 0.2
katG 2155869 p.Glu81Asp missense_variant 0.18
PPE35 2167985 p.Met876Ile missense_variant 0.18
PPE35 2170012 p.Arg201Trp missense_variant 0.27
Rv1979c 2222801 p.Phe122Leu missense_variant 0.2
Rv1979c 2223153 c.12G>T synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289909 c.-668G>A upstream_gene_variant 0.22
kasA 2518047 c.-68G>T upstream_gene_variant 0.13
pepQ 2859393 p.Leu342Phe missense_variant 0.18
pepQ 2859741 c.678C>A synonymous_variant 0.22
ribD 2987451 p.Arg205Ser missense_variant 0.15
thyX 3067969 c.-24G>A upstream_gene_variant 0.15
thyA 3073807 p.Arg222His missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086689 c.-131G>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473893 c.-114G>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612305 p.Ala271Asp missense_variant 0.17
fbiA 3640870 p.Ala110Pro missense_variant 0.17
rpoA 3878387 p.Thr41Ala missense_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039358 c.1347C>T synonymous_variant 0.22
clpC1 4039363 p.Ala448Ser missense_variant 0.22
clpC1 4039394 c.1311G>T synonymous_variant 0.22
panD 4044159 c.123C>A synonymous_variant 0.15
embC 4239952 c.90G>A synonymous_variant 0.22
embC 4240116 p.Thr85Asn missense_variant 0.29
embC 4240498 c.636G>T synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244280 p.Gly350Cys missense_variant 0.15
embA 4244371 p.Arg380His missense_variant 0.17
embA 4244613 p.Ala461Ser missense_variant 0.13
embB 4248253 c.1740C>A synonymous_variant 0.12
embB 4249606 c.3093C>A synonymous_variant 0.22
ubiA 4269935 c.-102C>A upstream_gene_variant 0.17
ethA 4327893 c.-420C>T upstream_gene_variant 0.13
ethR 4327925 p.Ala126Asp missense_variant 0.12
ethA 4328019 c.-546G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407801 c.402G>T synonymous_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408257 c.-55G>T upstream_gene_variant 0.2
gid 4408276 c.-74G>T upstream_gene_variant 0.18
gid 4408424 c.-222C>T upstream_gene_variant 0.17