TB-Profiler result

Run: SRR18715111
Summary

Run ID: SRR18715111

Sample name:

Date: 03-04-2023 20:19:19

Number of reads: 3997618

Percentage reads mapped: 98.81

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 6734 p.Asn499Asp missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288806 p.Ala146Thr missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_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 7173 p.Asp645Ala missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576116 p.Ala257Pro missense_variant 0.26
mshA 576119 p.Ala258Pro missense_variant 0.3
rpoB 761601 p.Ala599Thr missense_variant 1.0
rpoB 763045 p.Gln1080Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918478 p.Leu180Arg missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087084 p.Gln89Lys missense_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.67
fprA 3474737 p.Val244Gly missense_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.3
clpC1 4040230 p.Gly159Arg missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247395 c.882C>T synonymous_variant 1.0
embB 4248329 p.Met606Leu missense_variant 0.2
ethR 4328039 p.Arg164Pro missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>G upstream_gene_variant 1.0
whiB6 4338602 c.-81A>T upstream_gene_variant 1.0
gid 4408167 p.Phe12Leu missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0