TB-Profiler result

Run: SRR1062865
Summary

Run ID: SRR1062865

Sample name:

Date: 2024-04-16T07:54:48.657053

Number of reads: 356149

Percentage reads mapped: 4.57

Median coverage: 6.0

Strain: lineage2.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.56
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 0.97
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 0.84 rifampicin Not assoc w R - Interim
rpoB 762899 c.3093G>C synonymous_variant 0.83 rifampicin Not assoc w R - Interim
rpoB 762911 p.Ile1035Met missense_variant 0.86 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.82 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.82 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 0.82 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.8 rifampicin
rpoB 762942 c.3136_3138delATCinsGG frameshift_variant&missense_variant 0.78 rifampicin
rpoC 762947 c.-423C>G upstream_gene_variant 0.78 rifampicin
rpoC 762971 c.-399G>C upstream_gene_variant 0.77 rifampicin
rpoB 762989 c.3183G>T synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoB 762995 c.3189G>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 762998 c.-372G>A upstream_gene_variant 0.33 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764623 c.1254C>G synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.74 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.83 rifampicin Not assoc w R - Interim
rpoC 764665 c.1296C>G synonymous_variant 0.84 rifampicin
rpoC 764672 p.Gln435Thr missense_variant 0.84 rifampicin
rpoC 764686 c.1317C>T synonymous_variant 0.84 rifampicin
rpoC 764695 c.1326T>C synonymous_variant 0.81 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 764719 c.1350G>A synonymous_variant 0.65 rifampicin
rpoC 764722 c.1353G>C synonymous_variant 0.53 rifampicin
rpoC 764902 c.1533C>G synonymous_variant 0.63 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.74 rifampicin
rpoC 764912 p.Met515Val missense_variant 0.74 rifampicin
rpoC 764918 c.1549_1551delGTGinsAC frameshift_variant&missense_variant 0.74 rifampicin
rpoC 764935 c.1566T>C synonymous_variant 0.78 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoC 764953 c.1584G>C synonymous_variant 0.65 rifampicin
rpoC 764956 c.1587T>C synonymous_variant 0.65 rifampicin
rpoC 764958 p.Glu530Ala missense_variant 0.65 rifampicin
rpoC 764968 c.1599T>C synonymous_variant 0.65 rifampicin Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.91 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.91 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.96 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.9 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.76 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472709 n.864T>G non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.73 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.89 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.63 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.79 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.79 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.95 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.72 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.72 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3073953 c.519T>C synonymous_variant 0.74 para-aminosalicylic_acid
thyA 3073956 c.516G>C synonymous_variant 0.74 para-aminosalicylic_acid
thyA 3073959 c.513T>C synonymous_variant 0.74 para-aminosalicylic_acid
thyA 3073962 c.508_510delCTGinsAC frameshift_variant&missense_variant 0.71 para-aminosalicylic_acid
thyA 3073977 c.495A>G synonymous_variant 0.74 para-aminosalicylic_acid
thyA 3073989 c.483T>C synonymous_variant 0.74 para-aminosalicylic_acid
thyA 3073992 c.478_480delAGCinsTCG synonymous_variant 0.77 para-aminosalicylic_acid
thyA 3073999 p.Arg158Lys missense_variant 0.77 para-aminosalicylic_acid
thyA 3074004 c.468T>C synonymous_variant 0.74 para-aminosalicylic_acid
thyA 3074010 c.462C>G synonymous_variant 0.68 para-aminosalicylic_acid
thyA 3074031 c.441T>C synonymous_variant 0.48 para-aminosalicylic_acid