TB-Profiler result

Run: ERR4829816
Summary

Run ID: ERR4829816

Sample name:

Date: 2024-10-05T00:36:34.301953

Number of reads: 3036259

Percentage reads mapped: 86.36

Median coverage: 89.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1 Euro-American (S-type) None 1.0
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 1.0
lineage4.4 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 rpoB p.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761127 p.Ser441Ala missense_variant 0.19 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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 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
rpoB 761037 c.1231T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761084 c.1278C>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.13 rifampicin
rpoB 761096 c.1290G>C synonymous_variant 0.15 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.15 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.19 rifampicin
rpoB 761123 c.1317G>C synonymous_variant 0.15 rifampicin
rpoB 761126 c.1320G>C synonymous_variant 0.14 rifampicin
rpoB 761132 c.1326G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761159 c.1353G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762080 c.2274G>C synonymous_variant 0.1 rifampicin
rpoB 762085 p.Ala760Glu missense_variant 0.12 rifampicin
rpoB 762089 c.2283G>A synonymous_variant 0.13 rifampicin
rpoB 762114 p.Ile770Val missense_variant 0.12 rifampicin Uncertain significance
rpoB 762134 c.2328C>T synonymous_variant 0.14 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.16 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762156 p.Val784Ile missense_variant 0.16 rifampicin
rpoB 762167 c.2361T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762177 p.Arg791Thr missense_variant 0.14 rifampicin
rpoB 762181 p.Asp792Ala missense_variant 0.17 rifampicin
rpoB 762185 c.2379G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762194 c.2388G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762200 c.2394C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762224 c.2418C>T synonymous_variant 0.12 rifampicin
rpoC 763589 p.Ile74Val missense_variant 0.11 rifampicin
rpoC 763642 c.273G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763648 c.279C>T synonymous_variant 0.13 rifampicin
rpoC 763657 p.Glu96Asp missense_variant 0.16 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>T synonymous_variant 0.16 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763718 p.Leu117Val missense_variant 0.14 rifampicin
rpoC 763723 c.354G>C synonymous_variant 0.12 rifampicin
rpoC 763729 c.360G>C synonymous_variant 0.11 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.12 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.21 rifampicin
rpoC 763772 p.Val135Met missense_variant 0.16 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.1 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.42 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.42 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.57 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 0.42 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.42 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472685 n.840G>T non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472701 n.856T>C non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.27 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.39 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 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.34 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.51 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.51 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin
streptomycin
amikacin Uncertain significance
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.3 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 0.41 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.38 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 0.42 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.37 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473288 n.1443_1446delCTCGinsGGCTTGTCC non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.29 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834231 c.690T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834234 c.693G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834246 c.705G>T synonymous_variant 0.12 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834294 c.753G>C synonymous_variant 0.23 pyrazinamide
rpsA 1834298 p.Gln253Glu missense_variant 0.23 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834307 p.Asp256Gln missense_variant 0.2 pyrazinamide
rpsA 1834312 c.771G>A synonymous_variant 0.21 pyrazinamide
rpsA 1834327 c.786G>T synonymous_variant 0.2 pyrazinamide
rpsA 1834345 c.804C>T synonymous_variant 0.17 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834354 c.813G>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834360 c.819G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834361 c.820T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834378 c.837T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834387 c.846C>T synonymous_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
ndh 2102990 p.Val18Ala missense_variant 1.0 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2222074 p.Pro364Leu missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3065999 p.Arg65Ser missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_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