TB-Profiler result

Run: SRR13837695
Summary

Run ID: SRR13837695

Sample name:

Date: 03-04-2023 09:16:04

Number of reads: 294847

Percentage reads mapped: 97.34

Strain: lineage4.9

Drug-resistance: HR-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
lineage4.9 Euro-American (H37Rv-like) T1 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
katG 2154798 c.1313_1314insT frameshift_variant 1.0 isoniazid
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
gyrB 5906 p.Val223Leu missense_variant 1.0
gyrB 6011 p.Val258Met missense_variant 1.0
gyrB 6678 p.Pro480Arg missense_variant 1.0
fgd1 490676 c.-107G>C upstream_gene_variant 1.0
ccsA 620028 c.138G>C synonymous_variant 1.0
rpoB 759638 c.-169T>A upstream_gene_variant 1.0
rpoB 760454 c.650delG frameshift_variant 0.94
rpoB 762317 c.2511A>G synonymous_variant 0.2
rpoC 765487 p.Met706Ile missense_variant 1.0
mmpL5 775627 p.Trp952Gly missense_variant 0.2
rpsL 781409 c.-151T>A upstream_gene_variant 1.0
fbiC 1302873 c.-58A>T upstream_gene_variant 1.0
fbiC 1304811 c.1881C>G synonymous_variant 0.12
fbiC 1304817 c.1887T>C synonymous_variant 0.12
fbiC 1304829 c.1899T>C synonymous_variant 0.12
fbiC 1304856 c.1926C>G synonymous_variant 0.17
fbiC 1304893 p.Gly655Ser missense_variant 0.18
fbiC 1304910 c.1980G>C synonymous_variant 0.18
fbiC 1304916 c.1986T>C synonymous_variant 0.27
fbiC 1304928 c.1998T>C synonymous_variant 0.18
fbiC 1304937 c.2007G>C synonymous_variant 0.18
fbiC 1304958 c.2028T>G synonymous_variant 0.22
Rv1258c 1406178 p.Val388Ala missense_variant 0.22
rrs 1471874 n.29A>C non_coding_transcript_exon_variant 1.0
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.2
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.22
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.22
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.22
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.22
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.22
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.22
katG 2154654 p.Ser486Arg missense_variant 1.0
katG 2154882 c.1230G>A synonymous_variant 1.0
katG 2155857 c.255C>A synonymous_variant 1.0
PPE35 2170198 p.Ala139Ser missense_variant 1.0
pncA 2290069 c.-828C>T upstream_gene_variant 1.0
eis 2714922 c.411G>A synonymous_variant 1.0
thyA 3074067 c.405C>G synonymous_variant 1.0
fbiB 3642020 p.Asp162Glu missense_variant 0.25
alr 3840223 c.1198A>C synonymous_variant 1.0
alr 3840711 p.Ser237Leu missense_variant 1.0
clpC1 4039469 c.1236T>C synonymous_variant 0.18
clpC1 4039648 p.Glu353Gln missense_variant 1.0
embC 4242023 p.Val721Leu missense_variant 1.0
embA 4245071 c.1839G>A synonymous_variant 1.0
ethA 4327364 p.Lys37Arg missense_variant 1.0