TB-Profiler result

Run: ERR245804
Summary

Run ID: ERR245804

Sample name:

Date: 31-03-2023 18:22:30

Number of reads: 14824438

Percentage reads mapped: 99.41

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.27
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.32
rpoC 765150 p.Gly594Glu missense_variant 0.99
rpoC 767305 p.Tyr1312* stop_gained 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417501 c.-154A>C upstream_gene_variant 0.27
atpE 1461019 c.-26C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.22
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.21
fabG1 1673449 p.Thr4Pro missense_variant 0.38
inhA 1674892 p.Asn231Asp missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156096 p.Pro6Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.3
eis 2715586 c.-254G>C upstream_gene_variant 0.62
ahpC 2725954 c.-239C>T upstream_gene_variant 0.3
pepQ 2859381 c.1038C>G synonymous_variant 0.21
ribD 2987589 c.751C>T synonymous_variant 0.99
Rv2752c 3064741 p.Gly484Ala missense_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.25
fbiB 3641955 p.Gly141Arg missense_variant 0.23
fbiB 3642734 c.1200G>C synonymous_variant 0.18
ddn 3987013 p.Gly57Ala missense_variant 0.2
clpC1 4038857 c.1848C>A synonymous_variant 0.21
clpC1 4039363 p.Ala448Pro missense_variant 0.26
clpC1 4039932 p.Gly258Val missense_variant 0.37
embC 4241429 p.Phe523Val missense_variant 0.5
embC 4241456 p.Ala532Pro missense_variant 0.36
embC 4242476 p.Pro872Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embC 4242803 p.Val981Leu missense_variant 0.99
embC 4242822 p.Val987Gly missense_variant 0.28
embB 4249408 c.2895G>A synonymous_variant 0.99
embB 4249504 p.Gln997His missense_variant 0.19
ubiA 4269529 p.Ala102Gly missense_variant 0.17
ethA 4327672 c.-199G>A upstream_gene_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0