TB-Profiler result

Run: SRR20139551
Summary

Run ID: SRR20139551

Sample name:

Date: 03-04-2023 21:48:59

Number of reads: 3062965

Percentage reads mapped: 99.65

Strain: lineage4.1.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrB 6695 p.Ile486Leu missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288938 p.Ala102Pro missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.99 kanamycin, amikacin
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 5740 c.501G>C synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 490756 c.-27T>G upstream_gene_variant 0.19
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759611 c.-196G>C upstream_gene_variant 0.16
rpoB 759615 c.-192A>C upstream_gene_variant 0.2
rpoB 759620 c.-187A>C upstream_gene_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.16
fbiC 1303038 c.108T>G synonymous_variant 0.15
fbiC 1304159 p.Val410Gly missense_variant 0.23
fbiC 1304166 c.1236A>G synonymous_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472484 n.639A>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714425 p.Ala303Val missense_variant 0.34
eis 2715468 c.-136C>T upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.15
ahpC 2726350 p.Trp53Leu missense_variant 0.16
thyA 3074645 c.-174T>G upstream_gene_variant 0.2
thyA 3074648 c.-177T>G upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240188 p.Val109Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.19
ethA 4326060 p.Lys472* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407983 c.219delG frameshift_variant 1.0