TB-Profiler result

Run: ERR4821408
Summary

Run ID: ERR4821408

Sample name:

Date: 2024-10-05T14:02:41.131858

Number of reads: 2386447

Percentage reads mapped: 92.3

Median coverage: 72.0

Strain: lineage4.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
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 Drugs Confidence
gyrB 6907 c.1668C>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9648 p.Val783Met missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
nusG 734734 p.Ala161Thr missense_variant 1.0 rifampicin Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 762167 c.2361T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764263 c.894G>A synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764503 c.1134G>T synonymous_variant 0.12 rifampicin
rpoC 764509 c.1140G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764512 c.1143G>C synonymous_variant 0.14 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764530 c.1161C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.18 rifampicin
rpoC 764543 p.Thr392Ala missense_variant 0.2 rifampicin
rpoC 764548 c.1179G>C synonymous_variant 0.2 rifampicin
rpoC 764573 p.Leu402Ile missense_variant 0.2 rifampicin
rpoC 764578 c.1209C>G synonymous_variant 0.21 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.2 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.21 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.21 rifampicin
rpoC 764602 c.1233C>T synonymous_variant 0.24 rifampicin
rpoC 764605 c.1236G>T synonymous_variant 0.24 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764647 c.1278C>T synonymous_variant 0.15 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764653 c.1284G>C synonymous_variant 0.14 rifampicin
rpoC 764656 c.1287C>T synonymous_variant 0.13 rifampicin
rpoC 764662 c.1293G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764678 p.Lys437Gln missense_variant 0.1 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.99 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777320 c.1161C>G synonymous_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.69 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.69 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.69 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.72 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.88 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.28 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.35 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.32 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.87 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.77 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834294 c.753G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834298 p.Gln253Glu missense_variant 0.12 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834309 p.Asp256Glu missense_variant 0.11 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.39 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.25 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3611974 c.1143A>C synonymous_variant 0.97 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin