TB-Profiler result

Run: ERR4813523

Summary

Run ID: ERR4813523

Sample name:

Date: 16-08-2022 10:47:35

Number of reads: 701537

Percentage reads mapped: 99.07

Strain: lineage4.1.2.1

Drug-resistance: Other


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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 0.99
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 7570 p.Ala90Val missense_variant 0.5 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.4 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761275 p.Leu490Pro missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766419 p.Gln1017Arg missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779473 p.Gly162Arg missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303758 c.828G>C synonymous_variant 0.18
Rv1258c 1406527 c.811_813dupGGC conservative_inframe_insertion 0.12
atpE 1461036 c.-9G>T upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471877 n.32A>G non_coding_transcript_exon_variant 0.09
rrl 1475059 n.1402G>A non_coding_transcript_exon_variant 0.15
rpsA 1833510 c.-31delG upstream_gene_variant 1.0
katG 2154010 p.Asn701Ser missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715295 p.Trp13* stop_gained 0.13
Rv2752c 3065532 c.659delC frameshift_variant 1.0
Rv2752c 3065737 p.Asp152Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339200 p.Pro28Leu missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840630 p.Pro264Arg missense_variant 0.13
rpoA 3878630 c.-123G>C upstream_gene_variant 0.2
clpC1 4039552 p.Leu385Met missense_variant 0.12
embC 4241834 p.Arg658* stop_gained 0.12
embC 4242803 p.Val981Leu missense_variant 0.88
aftB 4267526 c.1311C>T synonymous_variant 0.12
aftB 4267812 p.Pro342Leu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0