TB-Profiler result

Run: SRR7535079
Summary

Run ID: SRR7535079

Sample name:

Date: 2024-10-04T12:03:34.068184

Number of reads: 432404

Percentage reads mapped: 3.47

Median coverage: 8.0

Strain: lineage4.6.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.97
lineage4 Euro-American None 1.0
lineage4.6.1.1 Euro-American RD724 1.0
lineage4.6.1 Euro-American (Uganda) RD724 0.98
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
rpoB 762894 c.3088C>T synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoB 762911 p.Ile1035Met missense_variant 0.79 rifampicin
rpoB 762923 c.3117C>G synonymous_variant 0.77 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoC 762932 c.-438G>T upstream_gene_variant 0.73 rifampicin
rpoB 762939 p.Met1045Leu missense_variant 0.71 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.71 rifampicin Uncertain significance
rpoC 762947 c.-423C>G upstream_gene_variant 0.73 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.76 rifampicin Not assoc w R - Interim
rpoB 762989 c.3183G>T synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.59 rifampicin
rpoC 764905 c.1536C>T synonymous_variant 0.66 rifampicin
rpoC 764911 c.1542A>C synonymous_variant 0.66 rifampicin
rpoC 764914 p.Met515Ile missense_variant 0.63 rifampicin Uncertain significance
rpoC 764918 p.Val517Ile missense_variant 0.63 rifampicin
rpoC 764939 c.1570C>T synonymous_variant 0.61 rifampicin
rpoC 764947 c.1578G>C synonymous_variant 0.54 rifampicin
rpoC 764948 c.1579_1581delTTGinsCTC synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 764953 c.1584G>T synonymous_variant 0.52 rifampicin
rpoC 764956 c.1587T>C synonymous_variant 0.5 rifampicin
rpoC 764958 p.Glu530Ala missense_variant 0.56 rifampicin
rpoC 764962 c.1593G>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
fbiC 1303622 p.Tyr231Cys missense_variant 0.92 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.98 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.98 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.97 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.97 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.97 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.96 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.96 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.47 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.47 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.93 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.93 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.92 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.93 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.97 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin