TB-Profiler result

Run: ERR11465604
Summary

Run ID: ERR11465604

Sample name:

Date: 2024-10-05T01:17:40.524063

Number of reads: 3192656

Percentage reads mapped: 97.81

Median coverage: 57.0

Strain: lineage4.8.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.98
lineage4.8.1 Euro-American (mainly T) RD219 0.98
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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)
ethambutol
pyrazinamide
streptomycin gid p.Glu60* Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
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
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)
gid 4408025 p.Glu60* stop_gained 0.98 streptomycin 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8339 c.1038A>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8340 p.Ala347Ser missense_variant 0.19 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8366 c.1065G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8378 c.1077C>T synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8382 p.Leu361Met missense_variant 0.17 levofloxacin
moxifloxacin
gyrA 8393 c.1092T>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8399 c.1098T>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8417 c.1116C>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8420 c.1119T>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8903 c.1602T>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8996 c.1695T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8998 p.Leu566Trp missense_variant 0.17 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9197 c.1896G>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 9200 c.1899A>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
hadA 731753 c.-177A>C upstream_gene_variant 0.14 isoniazid
hadA 731756 c.-174C>T upstream_gene_variant 0.16 isoniazid
hadA 731774 c.-156T>C upstream_gene_variant 0.19 isoniazid
nusG 734451 c.198G>C synonymous_variant 0.15 rifampicin
nusG 734454 c.201A>G synonymous_variant 0.15 rifampicin
nusG 734460 c.207G>C synonymous_variant 0.13 rifampicin
nusG 734580 c.327T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 760449 p.Thr215Leu missense_variant 0.18 rifampicin
rpoB 760460 c.654G>T synonymous_variant 0.22 rifampicin
rpoB 760463 c.657C>G synonymous_variant 0.22 rifampicin
rpoB 760475 c.669A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760490 c.684C>T synonymous_variant 0.16 rifampicin Not assoc w R
rpoB 761264 c.1458C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761282 c.1476C>G synonymous_variant 0.14 rifampicin
rpoB 761675 c.1869G>C synonymous_variant 0.15 rifampicin
rpoB 761690 c.1884G>C synonymous_variant 0.12 rifampicin
rpoB 761711 c.1905C>G synonymous_variant 0.12 rifampicin
rpoB 761747 c.1941G>C synonymous_variant 0.14 rifampicin
rpoB 761758 p.Tyr651Phe missense_variant 0.14 rifampicin
rpoB 761765 c.1959T>G synonymous_variant 0.14 rifampicin
rpoB 761772 p.His656Ala missense_variant 0.13 rifampicin
rpoB 761778 p.Asn658Asp missense_variant 0.12 rifampicin
rpoB 763136 c.3330C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763142 c.-228C>G upstream_gene_variant 0.14 rifampicin
rpoC 763492 c.123G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763657 c.288G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765121 c.1752G>C synonymous_variant 0.14 rifampicin
rpoC 765662 c.2293_2295delTTGinsCTC synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765673 p.Asp768Glu missense_variant 0.18 rifampicin
rpoC 765811 c.2442T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765814 c.2445A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765826 c.2457T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 765850 c.2481G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765871 c.2502T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765875 p.Val836Ile missense_variant 0.24 rifampicin Uncertain significance
rpoC 765899 c.2530C>T synonymous_variant 0.26 rifampicin
rpoC 765904 c.2535C>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 765991 c.2622C>A synonymous_variant 0.23 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 766009 c.2640G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766012 c.2643C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766453 c.3084G>T synonymous_variant 0.24 rifampicin
rpoC 766456 c.3087C>G synonymous_variant 0.23 rifampicin
rpoC 766469 c.3100C>T synonymous_variant 0.17 rifampicin
rpoC 766480 c.3111C>G synonymous_variant 0.16 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.19 rifampicin
rpoC 766484 p.Val1039Ile missense_variant 0.15 rifampicin Uncertain significance
rpoC 766843 c.3474T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766846 c.3477C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775910 c.2571G>C synonymous_variant 0.16 bedaquiline
clofazimine
mmpL5 775966 p.Ala839Ser missense_variant 0.15 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800480 c.-329G>T upstream_gene_variant 0.15 linezolid
rplC 800498 c.-311G>A upstream_gene_variant 0.19 linezolid
rplC 800516 c.-293G>C upstream_gene_variant 0.3 linezolid
rplC 800546 c.-263T>C upstream_gene_variant 0.3 linezolid
rplC 800570 c.-239C>G upstream_gene_variant 0.27 linezolid
rplC 800574 c.-235_-233delGTCinsACT upstream_gene_variant 0.26 linezolid
rplC 800594 c.-215C>G upstream_gene_variant 0.25 linezolid
rplC 800597 c.-212A>G upstream_gene_variant 0.25 linezolid
rplC 800600 c.-209G>C upstream_gene_variant 0.25 linezolid
rplC 800612 c.-197A>G upstream_gene_variant 0.21 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.21 linezolid
rplC 800645 c.-164C>G upstream_gene_variant 0.12 linezolid
fbiC 1303545 c.615A>G synonymous_variant 0.13 pretomanid
delamanid
clofazimine
fbiC 1303590 c.660A>G synonymous_variant 0.11 pretomanid
delamanid
clofazimine
fbiC 1303602 c.672A>G synonymous_variant 0.12 pretomanid
delamanid
clofazimine
Rv1258c 1407466 c.-126G>T upstream_gene_variant 0.17 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471985 n.140T>C non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1471996 n.151C>T non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.96 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674486 c.285T>C synonymous_variant 0.15 isoniazid
ethionamide
rpsA 1833886 c.345C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834297 c.756C>T synonymous_variant 0.2 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.17 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
rpsA 1834361 c.820T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>C synonymous_variant 0.26 pyrazinamide
rpsA 1834378 c.837T>C synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
rpsA 1834423 c.882G>C synonymous_variant 0.26 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.22 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.26 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.22 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170892 c.-280G>A upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518759 c.645C>G synonymous_variant 0.29 isoniazid
Rv2477c 2783344 c.699C>G synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783626 c.417G>C synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783656 c.387G>C synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.96 capreomycin
Rv2752c 3064998 c.1194A>C synonymous_variant 0.16 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065001 c.1191C>T synonymous_variant 0.21 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
fbiD 3339040 c.-78T>C upstream_gene_variant 0.98 pretomanid
delamanid
clofazimine
lpqB 3625849 c.-939T>C upstream_gene_variant 0.12 rifampicin
bedaquiline
mtrB 3625852 c.762A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625864 c.-954T>G upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3626969 c.-356C>G upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3626995 c.-382C>A upstream_gene_variant 0.19 rifampicin
bedaquiline
mtrB 3626999 c.-386G>C upstream_gene_variant 0.2 rifampicin
bedaquiline
mtrB 3627008 c.-395G>C upstream_gene_variant 0.24 rifampicin
bedaquiline
mtrB 3627011 c.-398T>G upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrB 3627017 c.-404G>A upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrA 3627811 c.-462T>G upstream_gene_variant 1.0 rifampicin
bedaquiline
fbiB 3642874 p.Leu447Arg missense_variant 0.93 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rpoA 3877818 c.690A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878118 c.390T>C synonymous_variant 0.12 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.12 rifampicin
clpC1 4038812 c.1893T>C synonymous_variant 0.13 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4268099 c.738G>C synonymous_variant 0.14 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R