TB-Profiler result

Run: SRR1049752
Summary

Run ID: SRR1049752

Sample name:

Date: 2024-10-04T04:00:49.488134

Number of reads: 1581000

Percentage reads mapped: 36.7

Median coverage: 32.0

Strain: lineage4.6.1.2

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 1.0
lineage4.6.1.2 Euro-American RD724 1.0
lineage4 Euro-American None 1.0
lineage4.6.1 Euro-American (Uganda) RD724 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
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 761155 p.Ser450Leu missense_variant 0.95 rifampicin Assoc w R
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 6501 p.Arg421His missense_variant 0.94 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 1.0 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
nusG 734624 p.Arg124Leu missense_variant 1.0 rifampicin Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762917 c.3111C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.21 rifampicin
rpoB 762934 c.3129_3130insAGCC frameshift_variant 0.2 rifampicin
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.2 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.21 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.23 rifampicin
rpoC 764587 c.1218C>G synonymous_variant 0.3 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.33 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 764663 p.Val432Thr missense_variant 0.39 rifampicin
rpoC 764672 p.Gln435Glu missense_variant 0.37 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.23 rifampicin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253900 p.Leu212Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
embR 1416410 p.Leu313Arg missense_variant 0.97 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.54 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.49 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.48 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.48 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.4 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.35 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.34 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.25 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.43 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.44 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 0.41 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 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.3 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474182 n.525C>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474185 n.528G>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474235 n.578delGinsAT non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.63 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.63 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
inhA 1674465 c.264C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154874 p.Tyr413Cys missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2681 2996876 c.138A>C synonymous_variant 1.0 capreomycin Not assoc w R
whiB7 3569029 c.-350A>G upstream_gene_variant 0.97 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
glpK 4139670 p.Cys29Tyr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embA 4245055 p.Thr608Asn missense_variant 1.0 ethambutol Uncertain significance
ethR 4328183 p.Tyr212Cys missense_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 4338635 c.-114A>C upstream_gene_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin