TB-Profiler result

Run: SRR7755642
Summary

Run ID: SRR7755642

Sample name:

Date: 2024-04-15T13:09:12.657576

Number of reads: 3824398

Percentage reads mapped: 96.62

Median coverage: 76.0

Strain: lineage4.2.1

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 1.0
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 1.0 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin Assoc w R
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
amikacin Uncertain significance Mutation from literature
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin Assoc w R
embB 4247402 p.Ser297Ala missense_variant 1.0 ethambutol Uncertain significance 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
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
fgd1 491247 c.465C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
ccsA 619969 p.Val27Ile missense_variant 1.0 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 1.0 rifampicin Uncertain significance
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
rplC 800204 c.-605T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12 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 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1475767 n.2110_2112delGGTinsTC non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.19 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 0.19 capreomycin
linezolid
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.1 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
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 2063685 c.1044G>A synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys 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
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.97 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
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
embB 4249594 c.3081G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ethA 4326632 p.His281Pro missense_variant 1.0 ethionamide Uncertain significance
ethA 4328376 c.-903G>C 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