TB-Profiler result

Run: SRR28351341
Summary

Run ID: SRR28351341

Sample name:

Date: 2024-05-22T12:17:56.791659

Number of reads: 11088562

Percentage reads mapped: 99.09

Median coverage: 355.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.1.1 Euro-American (X-type) RD183 0.97
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) 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 rrs n.462C>T Uncertain significance 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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.17 streptomycin 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 8855 c.1554C>G synonymous_variant 0.95 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.99 ethionamide Uncertain significance
rpoB 759574 c.-233C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoB 761057 c.1251G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761948 c.2142G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762008 c.2202C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765409 c.2040T>C synonymous_variant 0.13 rifampicin
rpoC 765421 c.2052C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.17 rifampicin
rpoC 765541 c.2172C>G synonymous_variant 0.18 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.16 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.17 rifampicin
rpoC 765580 c.2211G>C synonymous_variant 0.18 rifampicin
rpoC 765613 p.His748Gln missense_variant 0.2 rifampicin
rpoC 765625 c.2256C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765631 p.Asp754Glu missense_variant 0.19 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.17 rifampicin
rpoC 765751 c.2382C>G synonymous_variant 0.17 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.16 rifampicin Uncertain significance
rpoC 765772 c.2403C>G synonymous_variant 0.16 rifampicin
rpoC 765784 c.2415C>G synonymous_variant 0.15 rifampicin
rpoC 765787 c.2418C>T synonymous_variant 0.15 rifampicin
rpoC 765793 c.2424C>G synonymous_variant 0.16 rifampicin
rpoC 765796 c.2427C>T synonymous_variant 0.16 rifampicin
rpoC 765811 c.2442T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765814 c.2445A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765826 c.2457T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.14 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.13 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.14 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.14 rifampicin
rpoC 766864 c.3495G>C synonymous_variant 0.14 rifampicin
rpoC 766963 c.3594T>C synonymous_variant 0.14 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
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
fabG1 1673368 c.-72A>G upstream_gene_variant 1.0 ethionamide
isoniazid
rpsA 1833667 c.126C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.14 pyrazinamide
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
PPE35 2167921 c.2691dupC frameshift_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
ahpC 2726210 c.18T>C synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv2477c 2783914 c.129T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783929 c.114C>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783932 c.111C>T synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783938 c.105T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784204 c.-162A>C upstream_gene_variant 0.23 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784211 c.-169A>C upstream_gene_variant 0.31 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3064824 c.1368C>T synonymous_variant 1.0 ethambutol
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 0.99 rifampicin Not assoc w R
rpoA 3877613 p.Ile299Val missense_variant 0.14 rifampicin
rpoA 3877668 c.840A>G synonymous_variant 0.14 rifampicin
rpoA 3877692 c.816G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>C synonymous_variant 0.14 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878976 c.-469A>G upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878986 c.-479G>C upstream_gene_variant 0.14 rifampicin
rpoA 3878998 c.-491C>G upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoA 3879005 c.-499_-498delAAinsCG upstream_gene_variant 0.14 rifampicin
rpoA 3879013 c.-506A>G upstream_gene_variant 0.15 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.13 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.14 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.14 rifampicin
clpC1 4039589 c.1116G>C synonymous_variant 0.13 pyrazinamide
embC 4240897 c.1035C>G synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.96 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.28 ethambutol
embB 4248220 c.1707A>C synonymous_variant 0.14 ethambutol
embB 4249408 c.2895G>A synonymous_variant 0.94 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