TB-Profiler result

Run: ERR4796669
Summary

Run ID: ERR4796669

Sample name:

Date: 01-04-2023 07:01:05

Number of reads: 4240285

Percentage reads mapped: 99.56

Strain: lineage4.8;lineage3.1

Drug-resistance: HR-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
lineage3 East-African-Indian CAS RD750 0.82
lineage4 Euro-American LAM;T;S;X;H None 0.19
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.17
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.82
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 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.25 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.22 isoniazid
pncA 2288952 p.Gly97Val missense_variant 0.19 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.15 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 0.89
gyrA 9304 p.Gly668Asp missense_variant 0.86
gyrA 9788 c.2487C>T synonymous_variant 0.87
fgd1 491742 c.960T>C synonymous_variant 0.8
mshA 576108 p.Ala254Gly missense_variant 0.35
mshA 576113 p.Arg256Gly missense_variant 0.3
mshA 576482 p.Val379Leu missense_variant 0.11
rpoB 759746 c.-61C>T upstream_gene_variant 0.79
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoB 762888 p.His1028Tyr missense_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303428 c.498C>A synonymous_variant 0.92
fbiC 1304265 c.1335C>T synonymous_variant 0.87
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.73
PPE35 2167926 p.Leu896Ser missense_variant 0.77
PPE35 2170065 p.Ala183Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.81
pncA 2289365 c.-125delC upstream_gene_variant 0.87
ahpC 2726105 c.-88G>A upstream_gene_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 0.84
fbiD 3339734 p.Ala206Gly missense_variant 0.36
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.8
fbiB 3642005 c.471C>G synonymous_variant 0.81
rpoA 3878590 c.-84delC upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.32
clpC1 4040396 c.309C>T synonymous_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 0.84
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.13
embB 4246811 p.Gly100Ser missense_variant 0.27
embB 4248399 p.Leu629Pro missense_variant 0.87
ethA 4326912 p.Val188Ile missense_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.71