TB-Profiler result

Run: ERR028606

Summary

Run ID: ERR028606

Sample name:

Date: 31-03-2023 08:24:09

Number of reads: 781944

Percentage reads mapped: 99.41

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 0.18
lineage4.1.2 Euro-American T;H None 0.05
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.18 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.29
mshA 575679 p.Asn111Ser missense_variant 0.5
mshA 575907 p.Ala187Val missense_variant 0.4
mshA 576077 c.730C>T synonymous_variant 0.6
ccsA 620625 p.Ile245Met missense_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.43
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303174 p.Leu82Val missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473064 n.1219A>G non_coding_transcript_exon_variant 0.12
rrl 1474007 n.350A>C non_coding_transcript_exon_variant 0.2
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.38
PPE35 2167926 p.Leu896Ser missense_variant 0.57
PPE35 2169320 p.Leu431Phe missense_variant 0.27
PPE35 2169866 c.747G>C synonymous_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.29
ahpC 2726338 p.Val49Gly missense_variant 0.47
thyA 3073806 c.666C>G synonymous_variant 0.3
ald 3086742 c.-78A>C upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.25
Rv3236c 3613184 c.-68C>T upstream_gene_variant 0.2
fbiB 3641955 p.Gly141Arg missense_variant 0.5
embC 4239842 c.-21C>A upstream_gene_variant 0.33
embC 4242425 p.Arg855Gly missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.2
embA 4243346 c.114A>G synonymous_variant 0.2
embA 4243419 p.Val63Ile missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 0.3
embB 4246941 p.Pro143Leu missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 0.62
ubiA 4269529 p.Ala102Gly missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.23
gid 4407927 p.Glu92Asp missense_variant 0.33