TB-Profiler result

Run: ERR4816198
Summary

Run ID: ERR4816198

Sample name:

Date: 2024-03-26T16:05:39.747919

Number of reads: 13360012

Percentage reads mapped: 94.58

Median coverage: 247.0

Strain: lineage4.1.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 1.0
lineage4.1 Euro-American 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
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
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
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_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
rpsL 781421 c.-139C>A upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1304610 c.1680C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472092 n.247C>T non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472120 n.275G>A non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472245 n.400C>A non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.12 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472380 n.535G>A non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472506 n.661A>T non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.41 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473047 n.1202C>T non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473157 n.1312C>T non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473698 n.41G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473699 n.42A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1473833 n.176_177insT non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473874 n.217G>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473884 n.227C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473887 n.230T>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473889 n.232G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473898 n.241C>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474171 n.514C>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474355 n.698A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474806 n.1149A>G non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474822 n.1165G>T non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>A non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474927 n.1271delC non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475124 n.1467A>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475655 n.1998T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1475697 n.2040C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.46 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>C non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
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 2063894 p.Asn279His missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2784617 c.-575T>C upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624660 p.Ala84Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_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