TB-Profiler result

Run: SRR1175049
Summary

Run ID: SRR1175049

Sample name:

Date: 2024-04-15T00:30:10.998806

Number of reads: 190714

Percentage reads mapped: 42.23

Median coverage: 4.0

Strain: lineage4.8;lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.8 Euro-American (mainly T) RD219 0.12
lineage4.9 Euro-American (H37Rv-like) None 0.88
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 0.68 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
hadA 731774 c.-156T>C upstream_gene_variant 0.7 isoniazid
hadA 731789 c.-141A>G upstream_gene_variant 0.8 isoniazid
hadA 731792 c.-138G>A upstream_gene_variant 0.8 isoniazid
hadA 731801 c.-129C>G upstream_gene_variant 0.8 isoniazid
nusG 734421 c.168A>G synonymous_variant 0.7 rifampicin
nusG 734424 c.171G>A synonymous_variant 0.7 rifampicin
rpoB 760196 c.390C>G synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.67 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoB 760611 c.805T>C synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.69 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoB 762149 c.2343G>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoB 763166 c.3360A>G synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoC 763190 c.-180C>T upstream_gene_variant 0.67 rifampicin
rpoC 763202 c.-168A>G upstream_gene_variant 0.55 rifampicin
rpoC 763402 c.33C>G synonymous_variant 0.83 rifampicin
rpoC 763411 c.42T>G synonymous_variant 0.83 rifampicin Not assoc w R - Interim
rpoC 763414 c.45T>C synonymous_variant 0.83 rifampicin
rpoC 763486 c.117T>G synonymous_variant 0.75 rifampicin
rpoC 763492 c.123G>C synonymous_variant 0.75 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.67 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 763606 c.237C>T synonymous_variant 0.67 rifampicin
rpoC 765404 p.Leu679Val missense_variant 0.58 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.58 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.67 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>G synonymous_variant 0.67 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 766010 c.2641_2642delTCinsAG synonymous_variant 0.65 rifampicin
rpoC 766021 c.2652G>C synonymous_variant 0.71 rifampicin
rpoC 766027 c.2658G>C synonymous_variant 0.71 rifampicin
rpoC 766043 p.Gln892Glu missense_variant 0.73 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.46 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.75 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.75 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.75 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.82 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.69 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.82 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rplC 800618 c.-191T>C upstream_gene_variant 0.8 linezolid
rplC 800627 c.-182C>T upstream_gene_variant 0.82 linezolid
rplC 800648 c.-161A>T upstream_gene_variant 0.62 linezolid
rplC 801402 c.594T>C synonymous_variant 0.64 linezolid
rplC 801405 c.597T>C synonymous_variant 0.64 linezolid
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.73 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.57 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.67 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.67 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.73 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.67 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.64 capreomycin
linezolid Uncertain significance
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.57 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476105 n.2448_2449delGAinsT non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833790 c.249T>C synonymous_variant 0.7 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.75 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.82 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.8 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.79 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.79 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.75 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.75 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.8 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.83 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.73 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.75 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.67 pyrazinamide
rpsA 1834684 c.1143C>T synonymous_variant 0.6 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.57 pyrazinamide
PPE35 2170892 c.-280G>A upstream_gene_variant 1.0 pyrazinamide
Rv2477c 2783887 c.156C>G synonymous_variant 0.62 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
lpqB 3625594 c.-684T>C upstream_gene_variant 0.77 bedaquiline
rifampicin
lpqB 3625602 c.-692T>C upstream_gene_variant 0.7 bedaquiline
rifampicin
lpqB 3625612 c.-702G>C upstream_gene_variant 0.7 bedaquiline
rifampicin
mtrB 3625616 p.Arg333Ala missense_variant 0.7 bedaquiline
rifampicin
lpqB 3625624 c.-714C>G upstream_gene_variant 0.8 bedaquiline
rifampicin
mtrB 3625636 c.978C>G synonymous_variant 0.83 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625656 c.958T>C synonymous_variant 0.85 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3625663 c.-753G>C upstream_gene_variant 0.91 bedaquiline
rifampicin
mtrB 3625797 p.Val273Met missense_variant 0.83 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625806 c.808A>C synonymous_variant 0.82 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625807 c.807C>G synonymous_variant 0.82 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625837 c.777C>G synonymous_variant 0.91 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625849 c.-939T>C upstream_gene_variant 0.92 bedaquiline
rifampicin
mtrB 3625852 c.762A>G synonymous_variant 0.92 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625864 c.-954T>G upstream_gene_variant 0.9 bedaquiline
rifampicin
mtrB 3627167 c.-554T>C upstream_gene_variant 0.7 bedaquiline
rifampicin
mtrA 3627188 c.162A>G synonymous_variant 0.9 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627209 c.-596G>A upstream_gene_variant 0.91 bedaquiline
rifampicin
mtrA 3627242 c.108C>T synonymous_variant 0.9 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627254 c.-641C>T upstream_gene_variant 1.0 bedaquiline
rifampicin
rpoA 3877571 p.Pro313Ala missense_variant 0.64 rifampicin
rpoA 3877613 p.Ile299Val missense_variant 0.82 rifampicin
rpoA 3877656 c.852T>G synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.67 rifampicin
rpoA 3877679 p.Ala277Ser missense_variant 0.64 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.67 rifampicin Not assoc w R - Interim
rpoA 3877909 p.Asn200Ser missense_variant 0.8 rifampicin
rpoA 3877920 c.588G>C synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoA 3877923 c.585C>T synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.73 rifampicin
rpoA 3878001 c.507A>G synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoA 3878391 c.117T>C synonymous_variant 0.7 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.6 rifampicin
rpoA 3878424 c.84G>C synonymous_variant 0.58 rifampicin
rpoA 3878436 c.72A>G synonymous_variant 0.58 rifampicin
rpoA 3878938 c.-431T>C upstream_gene_variant 0.67 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.75 rifampicin
clpC1 4039064 c.1641C>T synonymous_variant 0.54 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.5 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.55 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.6 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.55 pyrazinamide Not assoc w R - Interim