TB-Profiler result

Run: ERR4798121
Summary

Run ID: ERR4798121

Sample name:

Date: 01-04-2023 08:08:33

Number of reads: 4177802

Percentage reads mapped: 99.71

Strain: lineage4.3.3

Drug-resistance: MDR-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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
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 5866 c.627C>A synonymous_variant 0.25
gyrA 6868 c.-434G>A upstream_gene_variant 0.12
gyrA 7308 p.Asp3His missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8161 p.Ile287Thr missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490928 p.Gly49Val missense_variant 0.13
fgd1 491121 p.Glu113Asp missense_variant 0.33
mshA 575587 c.240C>T synonymous_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.53
ccsA 620038 p.Pro50Ala missense_variant 0.2
ccsA 620568 c.678C>T synonymous_variant 0.15
ccsA 620702 p.Ala271Gly missense_variant 0.18
ccsA 620715 c.825C>T synonymous_variant 0.14
rpoB 760358 c.552C>T synonymous_variant 0.13
rpoC 764565 p.Leu399Arg missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765035 p.Arg556Cys missense_variant 0.18
rpoC 765947 p.Leu860Met missense_variant 0.18
rpoC 765999 c.2632delG frameshift_variant 0.11
rpoC 767183 p.Val1272Met missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775936 p.Asp849Asn missense_variant 0.11
mmpL5 776652 p.Ile610Asn missense_variant 0.1
mmpL5 777664 p.Ala273Pro missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474911 n.1254G>A non_coding_transcript_exon_variant 0.2
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.4
fabG1 1673558 p.His40Pro missense_variant 0.29
inhA 1674710 p.Ser170* stop_gained 0.12
rpsA 1833652 c.111C>T synonymous_variant 0.14
rpsA 1834366 c.825A>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918031 p.Lys31Met missense_variant 0.38
tlyA 1918481 p.Val181Gly missense_variant 0.18
ndh 2101781 p.Phe421Ser missense_variant 0.14
ndh 2101789 c.1254G>C synonymous_variant 0.12
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156408 c.-297C>T upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289254 c.-13G>A upstream_gene_variant 0.15
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714878 p.Asp152Ala missense_variant 0.25
ahpC 2726144 c.-48delG upstream_gene_variant 0.12
folC 2746340 p.Ala420Val missense_variant 1.0
ribD 2987124 p.Val96Ile missense_variant 0.12
Rv2752c 3064826 p.Asp456Tyr missense_variant 0.33
thyX 3067909 p.Ala13Thr missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086924 c.105C>A synonymous_variant 0.29
ald 3087583 p.Val255Asp missense_variant 0.12
ald 3087923 p.Ser368Arg missense_variant 0.12
fbiD 3339534 c.417C>T synonymous_variant 0.15
Rv3083 3449342 p.Ser280Phe missense_variant 0.22
Rv3083 3449470 p.Thr323Ala missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474470 p.Asn155Ser missense_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038677 c.2028G>T synonymous_variant 0.22
clpC1 4039862 c.843C>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243193 c.-40T>C upstream_gene_variant 0.17
embA 4243585 p.Phe118Ser missense_variant 0.13
embA 4243768 p.Val179Gly missense_variant 0.25
embA 4243832 c.600C>A synonymous_variant 0.15
embA 4243941 p.Leu237Met missense_variant 0.11
embA 4244479 p.Thr416Lys missense_variant 0.13
embB 4247024 p.Pro171Ala missense_variant 0.12
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4248512 p.Thr667Pro missense_variant 0.12
aftB 4268619 p.Val73Gly missense_variant 0.21
ethA 4326071 p.Ile468Thr missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0