TB-Profiler result

Run: ERR046917
Summary

Run ID: ERR046917

Sample name:

Date: 31-03-2023 08:56:58

Number of reads: 6801653

Percentage reads mapped: 99.41

Strain: lineage4.1.1.3.1

Drug-resistance: Pre-XDR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 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
gyrA 7581 p.Asp94His missense_variant 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288932 c.306_309delGTAC frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.74 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 9304 p.Gly668Asp missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.42
rpoC 762836 c.-534C>G upstream_gene_variant 0.31
rpoC 764725 p.Phe452Leu missense_variant 0.2
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 1303601 p.Glu224Gly missense_variant 1.0
Rv1258c 1406358 p.Ile328Thr missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.19
inhA 1674892 p.Asn231Asp missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.21
PPE35 2169866 c.747G>C synonymous_variant 0.37
PPE35 2170156 p.Ala153Pro missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.25
eis 2715586 c.-254G>C upstream_gene_variant 0.21
folC 2746186 c.1413G>C synonymous_variant 0.22
pepQ 2859381 c.1038C>G synonymous_variant 0.21
Rv2752c 3064552 p.Arg547Pro missense_variant 0.21
Rv2752c 3064741 p.Gly484Ala missense_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.2
fbiB 3641955 p.Gly141Arg missense_variant 0.26
rpoA 3878238 p.Asp90Glu missense_variant 0.19
ddn 3987013 p.Gly57Ala missense_variant 0.21
clpC1 4038857 c.1848C>A synonymous_variant 0.25
clpC1 4039932 p.Gly258Val missense_variant 0.26
embC 4239842 c.-21C>A upstream_gene_variant 0.14
embC 4239973 c.111T>G synonymous_variant 0.16
embC 4241456 p.Ala532Pro missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.28
embA 4244375 c.1143C>G synonymous_variant 0.23
embA 4245946 p.Ile905Thr missense_variant 0.18
embB 4248725 p.Ser738Ala missense_variant 0.29
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.25
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0