TB-Profiler result

Run: ERR4195751

Summary

Run ID: ERR4195751

Sample name:

Date: 01-04-2023 05:30:52

Number of reads: 724441

Percentage reads mapped: 99.54

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 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
gid 4408154 c.48delT frameshift_variant 1.0 streptomycin
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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576273 p.Pro309Leu missense_variant 0.14
ccsA 620029 c.139C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475395 n.1738T>C non_coding_transcript_exon_variant 1.0
rrl 1475842 n.2185C>T non_coding_transcript_exon_variant 0.2
rrl 1476135 n.2478T>G non_coding_transcript_exon_variant 0.12
fabG1 1673780 p.Thr114Ile missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067865 c.81C>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612739 p.Tyr126* stop_gained 0.11
fbiB 3640818 c.-717G>C upstream_gene_variant 0.12
fbiB 3642391 p.Ala286Glu missense_variant 0.12
rpoA 3878182 p.Asp109Gly missense_variant 0.1
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244443 p.Arg404Gln missense_variant 0.18
embA 4244924 c.1692G>T synonymous_variant 0.17
embB 4246567 c.54G>T synonymous_variant 0.12
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0