TB-Profiler result

Run: SRR1013528
Summary

Run ID: SRR1013528

Sample name:

Date: 2025-02-11T10:27:55.430863

Number of reads: 343445

Percentage reads mapped: 4.27

Median coverage: 7.0

Strain: lineage2.2.2;lineage4

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.29
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.47
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage4 Euro-American None 0.71
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid
ethambutol
pyrazinamide
streptomycin gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.93 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761110 p.Asp435Val missense_variant 0.82 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.59 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin Uncertain significance Mutation from literature
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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 762894 c.3088C>T synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoB 762899 c.3093G>C synonymous_variant 0.82 rifampicin Not assoc w R - Interim
rpoB 762911 p.Ile1035Met missense_variant 0.88 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.85 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.82 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.78 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.78 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.78 rifampicin Uncertain significance
rpoC 762947 c.-423C>G upstream_gene_variant 0.76 rifampicin
rpoC 762971 c.-399G>C upstream_gene_variant 0.71 rifampicin
rpoB 762989 c.3183G>T synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 764623 c.1254C>G synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.72 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.81 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.85 rifampicin Not assoc w R - Interim
rpoC 764665 c.1296C>G synonymous_variant 0.81 rifampicin
rpoC 764672 p.Gln435Thr missense_variant 0.84 rifampicin
rpoC 764686 c.1317C>T synonymous_variant 0.88 rifampicin
rpoC 764695 c.1326T>C synonymous_variant 0.91 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.85 rifampicin Not assoc w R - Interim
rpoC 764719 c.1350G>A synonymous_variant 0.75 rifampicin
rpoC 764722 c.1353G>C synonymous_variant 0.67 rifampicin
rpoC 764902 c.1533C>G synonymous_variant 0.71 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.74 rifampicin
rpoC 764912 p.Met515Val missense_variant 0.74 rifampicin
rpoC 764918 p.Val517Ile missense_variant 0.7 rifampicin
rpoC 764935 c.1566T>C synonymous_variant 0.75 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoC 764953 c.1584G>C synonymous_variant 0.74 rifampicin
rpoC 764956 c.1587T>C synonymous_variant 0.78 rifampicin
rpoC 764958 p.Glu530Ala missense_variant 0.78 rifampicin
rpoC 764968 c.1599T>C synonymous_variant 0.78 rifampicin Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
Rv1129c 1254669 c.-135C>G upstream_gene_variant 0.9 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.82 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 0.86 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.87 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.89 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.87 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.81 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.66 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.67 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.87 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 0.87 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.87 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.2 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 0.79 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.82 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 0.86 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
glpK 4139947 c.-192C>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R