TB-Profiler result

Run: ERR3078008
Summary

Run ID: ERR3078008

Sample name:

Date: 2024-10-04T20:22:09.280293

Number of reads: 872269

Percentage reads mapped: 4.86

Median coverage: 20.0

Strain: lineage4.6.1.1

Spoligotype:

Drug-resistance: MDR-TB

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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 0.97
lineage4.6.1.1 Euro-American RD724 0.27
lineage4.6.1 Euro-American (Uganda) RD724 0.93
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gly442Glu Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Leu443Ile Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Leu449Val Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid ahpC c.-54C>T Uncertain significance Mutation from literature
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 761131 p.Gly442Glu missense_variant 0.23 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761133 p.Leu443Ile missense_variant 0.23 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761151 p.Leu449Val missense_variant 0.21 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
ahpC 2726139 c.-54C>T upstream_gene_variant 0.82 isoniazid 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 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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
mshA 575110 c.-238C>T upstream_gene_variant 0.94 isoniazid
ethionamide
rpoB 761126 c.1320G>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761156 c.1350G>C synonymous_variant 0.21 rifampicin
rpoB 761159 c.1353G>A synonymous_variant 0.22 rifampicin
rpoB 761162 c.1356G>C synonymous_variant 0.21 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761168 c.1362C>G synonymous_variant 0.21 rifampicin
rpoB 761178 p.Ser458Thr missense_variant 0.21 rifampicin Uncertain significance
rpoB 761195 c.1389G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761196 p.Leu464Phe missense_variant 0.24 rifampicin
rpoB 761204 c.1398C>G synonymous_variant 0.25 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.29 rifampicin
rpoB 761220 p.Ser472Thr missense_variant 0.25 rifampicin
rpoB 761234 c.1428G>T synonymous_variant 0.25 rifampicin
rpoB 761235 p.Met477Val missense_variant 0.25 rifampicin
rpoB 762878 p.Ile1024Met missense_variant 0.53 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 0.51 rifampicin Uncertain significance
rpoB 762888 p.His1028Asn missense_variant 0.51 rifampicin
rpoB 762899 c.3093G>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoB 762911 p.Ile1035Met missense_variant 0.53 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 762930 p.Pro1042Ser missense_variant 0.5 rifampicin
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 0.49 rifampicin
rpoB 762939 p.Met1045Leu missense_variant 0.49 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.5 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.56 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.54 rifampicin
rpoB 762989 c.3183G>T synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Val missense_variant 0.42 rifampicin
rpoB 763014 p.Met1070Leu missense_variant 0.29 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 0.25 rifampicin
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 1472374 n.529T>A non_coding_transcript_exon_variant 0.43 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.37 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.39 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472694 n.849C>G non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.61 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.62 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.62 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.55 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472839 n.994C>G non_coding_transcript_exon_variant 0.48 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.95 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.95 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.95 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.94 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.84 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1475518 n.1861A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
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 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.95 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 0.95 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 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.94 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 0.95 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.91 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
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 2102116 c.927G>T synonymous_variant 0.96 isoniazid
delamanid
ethionamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726507 c.315G>T synonymous_variant 0.85 isoniazid
Rv2681 2996876 c.138A>C synonymous_variant 0.92 capreomycin Not assoc w R
whiB7 3569029 c.-350A>G upstream_gene_variant 1.0 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
glpK 4139670 p.Cys29Tyr missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4328329 c.-856C>G upstream_gene_variant 1.0 ethionamide
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