TB-Profiler result

Run: SRR5341258
Summary

Run ID: SRR5341258

Sample name:

Date: 04-04-2023 10:12:46

Number of reads: 1216814

Percentage reads mapped: 99.78

Strain: lineage4.9

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 0.95
lineage4.9 Euro-American (H37Rv-like) T1 None 0.88
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 1473246 n.1401A>G non_coding_transcript_exon_variant 0.92 kanamycin, capreomycin, aminoglycosides, amikacin
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 0.12
gyrA 7585 p.Ser95Thr missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 0.11
mshA 576117 p.Ala257Asp missense_variant 0.12
ccsA 620748 c.858T>G synonymous_variant 0.3
rpoB 761152 p.Leu449Gln missense_variant 0.11
mmpL5 776182 p.Asp767Asn missense_variant 0.12
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.14
Rv1258c 1406946 p.Ala132Gly missense_variant 0.14
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 0.2
katG 2155191 c.921A>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.34
PPE35 2170053 p.Thr187Ser missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.11
thyX 3067340 c.606G>A synonymous_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 0.15
embA 4243460 c.228C>T synonymous_variant 0.1
embB 4246544 p.Thr11Pro missense_variant 0.16
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.15
embB 4246567 c.54G>T synonymous_variant 0.14
aftB 4268810 c.27G>A synonymous_variant 0.13
gid 4407588 c.615A>G synonymous_variant 0.11