TB-Profiler result

Run: SRR6485170

Summary

Run ID: SRR6485170

Sample name:

Date: 04-04-2023 15:14:45

Number of reads: 2642728

Percentage reads mapped: 99.49

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.98
lineage4.4.1 Euro-American (S-type) S;T None 0.98
lineage4.4.1.1 Euro-American S;Orphans None 0.99
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
tlyA 1918571 c.637_638delCG frameshift_variant 1.0 capreomycin, capreomycin
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 0.97
gyrA 9304 p.Gly668Asp missense_variant 0.98
mshA 575464 c.117G>T synonymous_variant 0.97
mshA 576108 p.Ala254Gly missense_variant 0.43
mshA 576482 p.Val379Leu missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.11
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.97
PPE35 2169840 p.Gly258Asp missense_variant 0.98
PPE35 2170048 p.Leu189Val missense_variant 0.42
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170065 p.Ala183Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714384 c.945_948delCGAG frameshift_variant 0.98
folC 2747426 p.Gly58Ala missense_variant 0.37
ald 3086727 c.-93G>A upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fbiD 3339734 p.Ala206Gly missense_variant 0.2
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4246584 p.Arg24Pro missense_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0