TB-Profiler result

Run: ERR4829039
Summary

Run ID: ERR4829039

Sample name:

Date: 2024-04-15T07:01:31.905996

Number of reads: 2391947

Percentage reads mapped: 81.39

Median coverage: 73.0

Strain: lineage4.3.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.1 Euro-American (LAM) None 1.0
lineage4 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 c.1321_1323delTCGinsGC 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 c.1321_1323delTCGinsGC frameshift_variant&missense_variant 0.25 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 0.98 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 761030 c.1224G>C synonymous_variant 0.12 rifampicin
rpoB 761037 c.1231T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761084 c.1278C>A synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.22 rifampicin
rpoB 761096 c.1290G>C synonymous_variant 0.22 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.22 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.26 rifampicin
rpoB 761123 c.1317G>C synonymous_variant 0.25 rifampicin
rpoB 761126 c.1320G>C synonymous_variant 0.25 rifampicin
rpoB 761132 c.1326G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761159 c.1353G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>G synonymous_variant 0.12 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.11 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762156 c.2350_2352delGTGinsAC frameshift_variant&missense_variant 0.11 rifampicin
rpoB 762167 c.2361T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 763053 c.3247T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763648 c.279C>T synonymous_variant 0.11 rifampicin
rpoC 763657 p.Glu96Asp missense_variant 0.11 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764573 p.Leu402Ile missense_variant 0.26 rifampicin
rpoC 764578 c.1209C>G synonymous_variant 0.27 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.26 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.25 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.35 rifampicin
rpoC 764602 c.1233C>T synonymous_variant 0.37 rifampicin
rpoC 764605 c.1236G>T synonymous_variant 0.37 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764647 c.1278C>T synonymous_variant 0.26 rifampicin
rpoC 764650 c.1281G>C synonymous_variant 0.25 rifampicin
rpoC 764656 c.1287C>T synonymous_variant 0.29 rifampicin
rpoC 764662 c.1293G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764677 c.1308C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764678 p.Lys437Gln missense_variant 0.28 rifampicin
rpoC 764706 p.Leu446Gln missense_variant 0.27 rifampicin Uncertain significance
rpoC 764713 c.1344G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764731 c.1362G>C synonymous_variant 0.17 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.68 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.64 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.63 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.64 streptomycin
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.69 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.62 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.71 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.68 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443delCinsGTTTA non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.57 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1475760 n.2103_2107delCCGCAinsACCCCCCG non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.78 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.8 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.7 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834228 c.687C>T synonymous_variant 0.19 pyrazinamide
rpsA 1834234 c.693G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834246 c.705G>T synonymous_variant 0.22 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834294 c.753G>C synonymous_variant 0.32 pyrazinamide
rpsA 1834298 p.Gln253Glu missense_variant 0.32 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.32 pyrazinamide
rpsA 1834307 c.766_768delGACinsCG frameshift_variant&missense_variant 0.31 pyrazinamide Uncertain significance
rpsA 1834312 c.771G>A synonymous_variant 0.3 pyrazinamide
rpsA 1834327 c.786G>T synonymous_variant 0.27 pyrazinamide
rpsA 1834345 c.804C>T synonymous_variant 0.23 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834354 c.813G>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834360 c.819G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834361 c.820T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834378 c.837T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834387 c.846C>T synonymous_variant 0.18 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.14 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
bacA 2062840 p.Ala630Val missense_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
PPE35 2168412 p.Phe734Cys missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide 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 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R