TB-Profiler result

Run: SRR14781872
Summary

Run ID: SRR14781872

Sample name:

Date: 03-04-2023 11:03:10

Number of reads: 5603554

Percentage reads mapped: 99.73

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrA 7570 p.Ala90Val missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.97 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.96 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.99 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.98 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.19
mshA 576616 c.1269G>C synonymous_variant 0.15
rpoB 761277 p.Ile491Leu missense_variant 0.98
rpoC 764367 p.Gly333Ala missense_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.99
fbiC 1304962 p.Trp678Gly missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.32
rpsA 1834836 p.Met432Thr missense_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.97
PPE35 2170065 p.Ala183Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.99
kasA 2519071 p.Asp319Glu missense_variant 0.21
folC 2746340 p.Ala420Val missense_variant 0.99
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064823 p.Val457Leu missense_variant 0.16
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.42
fbiD 3339751 p.Ala212Pro missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
whiB7 3568425 c.255T>C synonymous_variant 0.27
whiB7 3568428 c.252A>G synonymous_variant 0.6
whiB7 3568431 c.249C>G synonymous_variant 0.27
rpoA 3878597 c.-90G>C upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.8
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 0.99
embC 4240409 p.Pro183Ala missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.47
embB 4248328 c.1815G>C synonymous_variant 0.2
ethA 4326843 p.Tyr211His missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.98