TB-Profiler result

Run: ERR4819359
Summary

Run ID: ERR4819359

Sample name:

Date: 01-04-2023 16:03:55

Number of reads: 793395

Percentage reads mapped: 99.69

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 2155168 p.Ser315Thr missense_variant 1.0 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
gyrB 6866 p.Leu543Met missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7810 c.513delC frameshift_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491463 p.Lys227Asn missense_variant 0.15
mshA 576011 p.Arg222Gly missense_variant 0.15
mshA 576024 p.Ser226* stop_gained 0.15
ccsA 620703 c.813G>A synonymous_variant 0.11
rpoB 762474 p.Gly890Ser missense_variant 0.17
rpoC 763953 p.Arg195His missense_variant 0.14
rpoC 764953 c.1584G>A synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766984 c.3615G>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776787 p.Glu565Gly missense_variant 0.14
mmpL5 776872 p.Glu537* stop_gained 0.12
mmpR5 778996 p.Val3Ile missense_variant 1.0
mmpR5 779026 p.Glu13Lys missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303663 c.733C>T synonymous_variant 0.2
fbiC 1304483 p.Ala518Asp missense_variant 0.17
fbiC 1304963 p.Trp678Leu missense_variant 0.15
embR 1417361 c.-14A>G upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471747 n.-99G>A upstream_gene_variant 0.29
rrs 1472223 n.378C>A non_coding_transcript_exon_variant 0.25
rrl 1473615 n.-43G>A upstream_gene_variant 0.17
rrl 1473764 n.107G>A non_coding_transcript_exon_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154299 p.Pro605Thr missense_variant 0.13
PPE35 2168331 p.Leu761Pro missense_variant 0.11
PPE35 2169052 p.Asn521Asp missense_variant 0.12
PPE35 2169617 p.Phe332Leu missense_variant 0.12
PPE35 2170400 c.213G>A synonymous_variant 0.17
PPE35 2170681 c.-69G>A upstream_gene_variant 1.0
Rv1979c 2222106 c.1059C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289239 c.3G>T start_lost 0.13
kasA 2517947 c.-168C>A upstream_gene_variant 0.12
kasA 2518046 c.-69C>A upstream_gene_variant 0.15
kasA 2518195 c.81G>A synonymous_variant 0.13
kasA 2518201 c.87C>T synonymous_variant 0.12
folC 2746726 p.Leu291Phe missense_variant 0.11
folC 2746807 c.792G>T synonymous_variant 0.13
Rv2752c 3064722 c.1470A>T synonymous_variant 0.11
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
thyX 3067911 p.Ile12Thr missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087441 p.Asp208Tyr missense_variant 0.13
Rv3083 3448539 c.36C>A synonymous_variant 0.17
Rv3083 3449137 c.634C>A synonymous_variant 0.15
Rv3083 3449397 p.Cys298* stop_gained 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568419 c.261C>T synonymous_variant 0.13
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612812 p.Thr102Lys missense_variant 0.11
Rv3236c 3613264 c.-148G>T upstream_gene_variant 0.12
fbiB 3642787 p.Trp418* stop_gained 0.12
alr 3840789 p.Gln211Arg missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040032 p.Val225Phe missense_variant 0.12
clpC1 4040071 p.Pro212Thr missense_variant 0.11
clpC1 4040078 p.Lys209Asn missense_variant 0.12
panD 4044373 c.-92C>A upstream_gene_variant 0.15
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4240107 p.Leu82Ser missense_variant 0.14
embC 4241709 p.Arg616Gln missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243209 c.-24C>T upstream_gene_variant 0.11
embA 4244354 c.1122G>A synonymous_variant 0.14
embA 4244648 c.1416G>C synonymous_variant 0.12
embB 4246895 p.Arg128Ser missense_variant 0.14
embB 4248361 c.1848A>G synonymous_variant 0.15
aftB 4266980 p.Asp619Glu missense_variant 0.12
ethR 4327723 p.Pro59Thr missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407889 p.Val105Glu missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0