TB-Profiler result

Run: ERR2041700
Summary

Run ID: ERR2041700

Sample name:

Date: 18-08-2022 09:23:30

Number of reads: 559925

Percentage reads mapped: 98.83

Strain: lineage4.2.2.1

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 0.99
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.1 Euro-American 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 761155 p.Ser450Trp missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289171 p.Gly24Asp missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7615 p.Leu105Arg missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9525 p.Val742Leu missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 759628 c.-179C>T upstream_gene_variant 0.11
rpoB 759711 c.-95_-88delGCCGAAAC upstream_gene_variant 0.12
rpoB 759726 c.-81A>T upstream_gene_variant 0.11
rpoB 759727 c.-80A>T upstream_gene_variant 0.11
rpoB 759730 c.-77A>G upstream_gene_variant 0.11
rpoB 759733 c.-74_-73insGTTTCGGC upstream_gene_variant 0.12
rpoB 760993 p.Glu396Val missense_variant 0.14
rpoB 762754 p.Leu983Ser missense_variant 0.13
rpoC 766891 c.3527delT frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801297 c.489C>G synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475241 n.1584C>G non_coding_transcript_exon_variant 1.0
rrl 1475607 n.1950A>G non_coding_transcript_exon_variant 0.13
fabG1 1673221 c.-219C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155596 c.516G>C synonymous_variant 0.11
kasA 2518638 p.Ser175* stop_gained 0.17
folC 2746138 c.1461A>G synonymous_variant 0.14
thyA 3074602 c.-131G>A upstream_gene_variant 0.11
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339158 p.Ile14Thr missense_variant 0.12
fbiD 3339215 p.Gln33Leu missense_variant 0.13
embC 4242623 p.Gly921Cys missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242702 p.Ala947Val missense_variant 0.14
embA 4244958 p.Ala576Thr missense_variant 1.0
embB 4246658 p.Val49Ile missense_variant 0.12
embB 4249535 c.3025delA frameshift_variant 0.15
embB 4249605 p.Gly1031Asp missense_variant 0.15