TB-Profiler result

Run: ERR038741
Summary

Run ID: ERR038741

Sample name:

Date: 31-03-2023 08:41:17

Number of reads: 10835450

Percentage reads mapped: 99.41

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
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
rpoB 761139 p.His445Asp missense_variant 0.99 rifampicin
pncA 2288779 c.459_462dupCAGG frameshift_variant 0.99 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.99 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
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 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 762249 p.Leu815Val missense_variant 0.21
rpoC 762836 c.-534C>G upstream_gene_variant 0.29
rpoC 764613 p.Gln415Arg missense_variant 1.0
rpoC 766163 p.Glu932Lys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.26
rrl 1474900 n.1243G>T non_coding_transcript_exon_variant 0.97
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.22
rpsA 1834013 p.Val158Leu missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154224 p.Gly630Arg missense_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 1.0
PPE35 2169068 c.1545G>T synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.15
PPE35 2169866 c.747G>C synonymous_variant 0.39
Rv1979c 2221919 p.Val416Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.37
eis 2714929 p.Thr135Ser missense_variant 1.0
eis 2715270 c.63G>C synonymous_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.21
ribD 2987307 p.Ala157Pro missense_variant 0.18
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.31
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.26
fbiB 3642734 c.1200G>C synonymous_variant 0.18
fbiB 3642772 p.Asp413Ala missense_variant 0.32
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.29
embC 4239842 c.-21C>A upstream_gene_variant 0.24
embC 4242425 p.Arg855Gly missense_variant 0.22
embC 4242476 p.Pro872Ala missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.39
ubiA 4269529 p.Ala102Gly missense_variant 0.28
ethA 4327672 c.-199G>A upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408072 p.Leu44Arg missense_variant 0.99