TB-Profiler result

Run: ERR553047
Summary

Run ID: ERR553047

Sample name:

Date: 02-08-2023 08:58:39

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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 6394 c.1157delA frameshift_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7390 p.Asp30Val missense_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9787 p.Asp829Val missense_variant 0.15
mshA 576351 p.Asp335Gly missense_variant 0.15
rpoB 762198 p.Gly798Ser missense_variant 0.12
rpoC 764051 p.Lys228Glu missense_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765362 p.Glu665Lys missense_variant 0.18
rpoC 767178 p.Ile1270Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779121 c.-641C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801391 p.Lys195Glu missense_variant 0.12
fbiC 1302954 c.24G>A synonymous_variant 0.88
embR 1417506 c.-159T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472854 n.1009G>A non_coding_transcript_exon_variant 0.12
rrl 1474116 n.459G>A non_coding_transcript_exon_variant 0.12
rpsA 1833799 c.258C>T synonymous_variant 0.15
rpsA 1834293 p.Val251Glu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154678 c.1434G>C synonymous_variant 1.0
katG 2156017 p.Gly32Val missense_variant 0.13
PPE35 2169405 p.Asn403Ser missense_variant 1.0
PPE35 2169854 c.759T>G synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726409 p.Asp73His missense_variant 1.0
folC 2746745 p.Val285Gly missense_variant 0.33
folC 2746961 p.Ala213Val missense_variant 0.25
Rv2752c 3065091 c.1101A>G synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087555 p.Ala246Pro missense_variant 0.33
fbiD 3339273 c.156T>G synonymous_variant 0.29
fprA 3473833 c.-174G>C upstream_gene_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613012 c.105G>A synonymous_variant 0.33
fbiB 3641614 c.83_105delATCTGAGCGCCGCCGTCGCCGCG frameshift_variant 0.22
fbiB 3641823 p.Asn97Asp missense_variant 0.33
rpoA 3878424 c.84G>T synonymous_variant 0.25
embC 4240646 p.Phe262Val missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249678 c.3165C>A synonymous_variant 1.0
aftB 4267857 p.Ile327Asn missense_variant 0.4
ethR 4327168 c.-381G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0