TB-Profiler result

Run: SRR1049743
Summary

Run ID: SRR1049743

Sample name:

Date: 2024-04-15T19:30:27.487107

Number of reads: 1999823

Percentage reads mapped: 40.61

Median coverage: 43.0

Strain: lineage4.6.1.1

Spoligotype:

Drug-resistance: Sensitive

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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 Euro-American None 1.0
lineage4.6.1.1 Euro-American RD724 0.76
lineage4.6.1 Euro-American (Uganda) RD724 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 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
rpoB 762899 c.3093G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762917 c.3111C>G synonymous_variant 0.2 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 0.2 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.21 rifampicin
rpoB 762939 c.3133_3135delATGinsCC frameshift_variant&missense_variant 0.22 rifampicin
rpoB 762942 c.3136_3138delATCinsGT frameshift_variant&missense_variant 0.22 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.12 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.34 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.31 rifampicin
rpoC 764587 c.1218C>G synonymous_variant 0.36 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
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 1472172 n.327T>C non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.63 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.76 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 0.62 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.61 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.49 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2681 2996876 c.138A>C synonymous_variant 1.0 capreomycin Not assoc w R
whiB7 3569029 c.-350A>G upstream_gene_variant 1.0 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
glpK 4139297 c.459G>A synonymous_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139670 p.Cys29Tyr missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid 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 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