TB-Profiler result

Run: ERR3077953

Summary

Run ID: ERR3077953

Sample name:

Date: 01-04-2023 00:12:27

Number of reads: 487992

Percentage reads mapped: 99.48

Strain: lineage4.2.2.2

Drug-resistance: Other


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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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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
tlyA 1918634 c.698delC frameshift_variant 0.12 capreomycin, capreomycin
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 7019 p.Gly594Trp missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 8853 p.Val518Phe missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490981 c.199C>A synonymous_variant 0.29
mshA 575760 p.Arg138His missense_variant 0.15
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576181 p.Lys278Asn missense_variant 0.12
ccsA 620107 p.Asp73Tyr missense_variant 0.17
ccsA 620236 p.Leu116Met missense_variant 0.12
rpoB 759615 c.-192A>C upstream_gene_variant 0.36
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoB 761900 c.2094C>T synonymous_variant 0.17
rpoB 762080 c.2274G>T synonymous_variant 0.2
rpoB 762300 p.Lys832Glu missense_variant 0.11
rpoC 766759 c.3390G>T synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303180 p.Ile84Val missense_variant 0.18
fbiC 1303197 p.Lys89Asn missense_variant 0.17
fbiC 1303307 p.Asp126Gly missense_variant 0.1
fbiC 1304689 c.1759C>A synonymous_variant 0.2
Rv1258c 1406981 c.360C>A synonymous_variant 0.13
Rv1258c 1407458 c.-118G>T upstream_gene_variant 0.15
embR 1416681 p.Asp223Asn missense_variant 0.13
embR 1416687 p.Gln221Lys missense_variant 0.13
embR 1417059 p.Ala97Ser missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471844 n.-2G>T upstream_gene_variant 0.13
rrs 1473367 n.1522G>A non_coding_transcript_exon_variant 0.13
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.11
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 1.0
rrl 1475346 n.1689C>A non_coding_transcript_exon_variant 0.14
rrl 1476768 n.3111G>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101867 c.1176C>A synonymous_variant 0.12
katG 2154860 c.1252C>A synonymous_variant 0.12
katG 2155957 p.Pro52Gln missense_variant 0.12
Rv1979c 2222657 p.Lys170Glu missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289118 p.His42Asn missense_variant 0.13
pncA 2289637 c.-396G>T upstream_gene_variant 0.12
kasA 2518151 p.Ser13Arg missense_variant 0.23
eis 2715452 c.-120G>T upstream_gene_variant 0.13
pepQ 2859900 p.Ser173Arg missense_variant 0.2
pepQ 2859983 p.Ala146Ser missense_variant 0.25
Rv2752c 3065975 p.Asp73Asn missense_variant 0.15
Rv2752c 3066279 c.-89_-88delCAinsTG upstream_gene_variant 0.12
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338919 c.-199C>A upstream_gene_variant 0.15
Rv3083 3448496 c.-8C>A upstream_gene_variant 0.12
Rv3083 3448525 p.Leu8Met missense_variant 0.12
Rv3083 3448808 p.Leu102Pro missense_variant 0.17
Rv3083 3448996 p.His165Asn missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474952 p.Gln316Lys missense_variant 0.12
whiB7 3568647 c.33C>A synonymous_variant 0.14
whiB7 3568789 c.-110A>G upstream_gene_variant 0.15
Rv3236c 3612913 c.204G>A synonymous_variant 0.15
Rv3236c 3612937 c.180C>A synonymous_variant 0.33
clpC1 4038474 p.Ser744Ile missense_variant 0.17
clpC1 4038912 p.Pro598Gln missense_variant 0.15
embC 4240625 p.Asp255Tyr missense_variant 0.22
embC 4240648 c.786C>T synonymous_variant 0.22
embC 4240655 p.Ala265Pro missense_variant 0.25
embC 4241747 p.Val629Leu missense_variant 0.15
embA 4242337 c.-896C>A upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242801 p.Pro980Gln missense_variant 0.15
embA 4244474 c.1242G>T synonymous_variant 0.22
embB 4247361 p.Val283Ala missense_variant 0.15
aftB 4268312 p.Leu175Phe missense_variant 0.13
ethA 4326789 p.Leu229Met missense_variant 0.18
ethR 4326925 c.-624A>G upstream_gene_variant 0.12
ethR 4327066 c.-483C>A upstream_gene_variant 0.2
ethA 4327316 p.Ile53Thr missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0