TB-Profiler result

Run: SRR1173861
Summary

Run ID: SRR1173861

Sample name:

Date: 03-04-2023 03:33:28

Number of reads: 3923791

Percentage reads mapped: 99.41

Strain: lineage4.8;lineage4.1.1.3

Drug-resistance: MDR-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 0.45
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.59
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.4
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.42
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.59 streptomycin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.37 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.38 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 0.44 pyrazinamide
pncA 2289067 p.Ser59Pro missense_variant 0.62 pyrazinamide
ald 3087278 c.464delG frameshift_variant 0.49 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 0.38 ethambutol
embB 4247429 p.Met306Val missense_variant 0.7 ethambutol
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.32 ethionamide
ethA 4326604 c.869dupA frameshift_variant 0.3 ethionamide, ethionamide
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 6815 p.Lys526Gln missense_variant 0.58
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.43
gyrA 9304 p.Gly668Asp missense_variant 0.4
rpoB 762285 p.Arg827Cys missense_variant 0.47
rpoC 765150 p.Gly594Glu missense_variant 0.54
rpoC 766485 p.Val1039Ala missense_variant 0.54
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 0.39
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154769 p.Asp448Ala missense_variant 0.54
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.44
alr 3840764 c.657G>C synonymous_variant 0.6
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.4
embB 4249408 c.2895G>A synonymous_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 0.28