TB-Profiler result

Run: ERR4813303
Summary

Run ID: ERR4813303

Sample name:

Date: 01-04-2023 12:39:49

Number of reads: 354774

Percentage reads mapped: 99.71

Strain: lineage4

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
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.Ser450Trp missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288885 p.Trp119Cys 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7406 c.105G>C synonymous_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9078 p.Gly593Trp missense_variant 0.2
gyrA 9189 p.Gly630Arg missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9349 p.Phe683Ser missense_variant 0.1
mshA 576719 p.Glu458* stop_gained 0.22
ccsA 620290 p.Tyr134His missense_variant 1.0
rpoB 763032 p.Ala1076Ser missense_variant 0.2
rpoC 763414 c.45T>C synonymous_variant 0.13
rpoC 764744 p.Arg459Trp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766724 p.His1119Asn missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776280 p.Arg734Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303857 c.927C>A synonymous_variant 0.29
fbiC 1304671 p.Val581Ile missense_variant 0.13
Rv1258c 1406645 c.696C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 1.0
rpsA 1833923 p.Gly128Ser missense_variant 0.12
PPE35 2168947 p.Pro556Thr missense_variant 0.14
PPE35 2169888 p.Phe242Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2715423 c.-91G>T upstream_gene_variant 0.17
pepQ 2859736 p.Gly228Glu missense_variant 1.0
Rv2752c 3065300 c.891dupC frameshift_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449854 p.Met451Val missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474691 p.Glu229* stop_gained 0.2
Rv3236c 3612574 c.543G>A synonymous_variant 0.15
alr 3840328 c.1093T>C synonymous_variant 0.5
rpoA 3877775 p.Ala245Ser missense_variant 0.13
ddn 3986983 c.145_147dupCTG conservative_inframe_insertion 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039625 p.Lys360Asn missense_variant 0.17
embC 4242251 p.Asp797Asn missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243227 c.-6_-5insGCCTCGT upstream_gene_variant 0.29
ethR 4327819 p.Ala91Ser missense_variant 0.14
whiB6 4338400 p.Trp41Leu missense_variant 0.14
whiB6 4338416 p.Gln36Lys missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0