TB-Profiler result

Run: SRR13861284
Summary

Run ID: SRR13861284

Sample name:

Date: 2024-10-04T13:26:40.464378

Number of reads: 423723

Percentage reads mapped: 7.07

Median coverage: 13.0

Strain: lineage4.9

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 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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.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
ethambutol
pyrazinamide
streptomycin rrs n.277G>C Mutation from literature
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 0.4 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761133 p.Leu443Ile missense_variant 0.4 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761151 p.Leu449Val missense_variant 0.42 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rrs 1472122 n.277G>C non_coding_transcript_exon_variant 0.79 streptomycin 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
gyrB 5319 p.Arg27Leu missense_variant 1.0 levofloxacin
moxifloxacin
mshA 575032 c.-316A>G upstream_gene_variant 1.0 isoniazid
ethionamide
rpoB 760867 p.Gly354Asp missense_variant 1.0 rifampicin
rpoB 761126 c.1320G>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761129 c.1323G>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 761156 c.1350G>C synonymous_variant 0.4 rifampicin
rpoB 761162 c.1356G>C synonymous_variant 0.4 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 761168 c.1362C>G synonymous_variant 0.44 rifampicin
rpoB 761178 p.Ser458Thr missense_variant 0.5 rifampicin Uncertain significance
rpoB 761192 c.1386C>G synonymous_variant 0.5 rifampicin
rpoB 761195 c.1389G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 761196 p.Leu464Phe missense_variant 0.44 rifampicin
rpoB 761204 c.1398C>T synonymous_variant 0.44 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.44 rifampicin
rpoB 761213 c.1407G>A synonymous_variant 0.47 rifampicin
rpoB 761220 p.Ser472Thr missense_variant 0.47 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 761235 p.Met477Val missense_variant 0.5 rifampicin
rpoC 764793 p.Met475Arg missense_variant 1.0 rifampicin
rpoC 766563 p.Thr1065Ser missense_variant 1.0 rifampicin
mmpL5 775976 c.2505G>C synonymous_variant 1.0 bedaquiline
clofazimine
mmpL5 776814 p.Gln556Arg missense_variant 1.0 bedaquiline
clofazimine
rplC 800623 c.-186A>C upstream_gene_variant 1.0 linezolid
rplC 800769 c.-40A>T upstream_gene_variant 1.0 linezolid
Rv1129c 1253289 c.1246C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
fbiC 1302878 c.-53C>G upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1303535 p.Ser202Leu missense_variant 1.0 pretomanid
delamanid
clofazimine
Rv1258c 1407569 c.-229C>A upstream_gene_variant 1.0 streptomycin
pyrazinamide
isoniazid
atpE 1461256 p.Met71Arg missense_variant 1.0 bedaquiline
rrs 1471836 n.-10A>G upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.32 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33 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 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.92 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 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.94 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 0.94 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 0.94 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
bacA 2063043 c.1686T>A synonymous_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
katG 2156157 c.-46C>A upstream_gene_variant 1.0 isoniazid
PPE35 2168627 p.Ile662Met missense_variant 1.0 pyrazinamide
pncA 2289242 c.-1T>C upstream_gene_variant 1.0 pyrazinamide
Rv2477c 2783664 c.378delA frameshift_variant 1.0 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
ribD 2987205 p.Ser123Ala missense_variant 1.0 para-aminosalicylic_acid
ribD 2987347 p.Pro170Leu missense_variant 1.0 para-aminosalicylic_acid
Rv2680 2995859 c.-246C>A upstream_gene_variant 1.0 capreomycin
Rv2681 2997492 p.Val252Phe missense_variant 1.0 capreomycin
Rv3083 3448903 p.Asp134His missense_variant 1.0 ethionamide
lpqB 3624372 p.Val180Ala missense_variant 1.0 rifampicin Uncertain significance
bedaquiline
mtrA 3627051 p.Asp100Val missense_variant 1.0 rifampicin
bedaquiline
embC 4241256 p.Arg465Thr missense_variant 1.0 ethambutol Uncertain significance
aftB 4268192 c.645G>C synonymous_variant 1.0 ethambutol