TB-Profiler result

Run: SRR069989
Summary

Run ID: SRR069989

Sample name:

Date: 2024-10-05T07:30:41.377736

Number of reads: 1366546

Percentage reads mapped: 76.26

Median coverage: 22.0

Strain: lineage2.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.74
lineage2.2 East-Asian (Beijing) RD105;RD207 0.81
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG c.1002_1003dupGA Assoc w R High-level resistance
kasA p.Asp66Asn Mutation from literature
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.89 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155108 c.1002_1003dupGA frameshift_variant 0.86 isoniazid Assoc w R High-level resistance
kasA 2518310 p.Asp66Asn missense_variant 1.0 isoniazid 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
dnaA 750 c.750C>G synonymous_variant 0.18 isoniazid
dnaA 756 c.756T>C synonymous_variant 0.18 isoniazid
gyrA 6778 c.-524C>T upstream_gene_variant 0.18 levofloxacin
moxifloxacin
gyrB 6793 c.1554T>C synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6797 p.Gly520Thr missense_variant 0.21 levofloxacin
moxifloxacin
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 8156 c.855T>C synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 8198 c.897T>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8207 c.906T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8219 c.918T>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8225 c.924T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8294 c.993T>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8420 c.1119T>C synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 8423 c.1122G>C synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9674 c.2373T>C synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 9677 c.2376C>T synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 9701 c.2400T>C synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9704 c.2403T>C synonymous_variant 0.3 levofloxacin
moxifloxacin
gyrA 9708 c.2407T>C synonymous_variant 0.26 levofloxacin
moxifloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 760253 c.447T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760946 c.1140A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 760970 c.1164G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.19 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.34 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 763028 c.3222T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.75 rifampicin Not assoc w R
rpoB 763031 c.3225T>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.24 rifampicin
rpoC 763158 c.-212C>T upstream_gene_variant 0.26 rifampicin
rpoC 763456 c.87A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763468 c.99G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764059 c.690G>C synonymous_variant 0.28 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.3 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764110 c.741C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.19 rifampicin
rpoC 764161 c.792G>C synonymous_variant 0.19 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764365 c.996C>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.47 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765508 c.2139C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 765541 c.2172C>G synonymous_variant 0.35 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.24 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.24 rifampicin
rpoC 765625 c.2256C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 765628 c.2259G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765631 p.Asp754Glu missense_variant 0.27 rifampicin
rpoC 765658 c.2289C>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 765700 c.2331T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 765892 c.2523T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766583 p.Gly1072Ser missense_variant 0.26 rifampicin
rpoC 766588 c.3219G>A synonymous_variant 0.26 rifampicin
rpoC 766591 c.3222A>G synonymous_variant 0.24 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.25 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 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781682 c.123T>C synonymous_variant 0.24 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.26 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.18 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.27 streptomycin
rpsL 781793 c.234G>C synonymous_variant 0.24 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.24 streptomycin
rplC 800648 c.-161A>C upstream_gene_variant 0.19 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.16 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303846 p.Phe306Val missense_variant 0.21 pretomanid
delamanid
clofazimine
fbiC 1303854 c.924T>C synonymous_variant 0.24 pretomanid
delamanid
clofazimine
fbiC 1303860 c.930A>C synonymous_variant 0.27 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1473981 n.324delGinsTT non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833595 c.54T>C synonymous_variant 0.23 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.38 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.34 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.38 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.31 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.26 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.28 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.23 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.28 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.31 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.36 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.32 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.28 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.26 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.26 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834297 c.756C>G synonymous_variant 0.21 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.19 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834606 c.1065C>G synonymous_variant 0.24 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834622 c.1081_1083delTCGinsAGC synonymous_variant 0.22 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.21 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
ndh 2101924 c.1119T>G synonymous_variant 0.25 isoniazid
delamanid
ethionamide
ndh 2101939 c.1104A>C synonymous_variant 0.3 isoniazid
delamanid
ethionamide
ndh 2101960 c.1083A>G synonymous_variant 0.34 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2517947 c.-168C>T upstream_gene_variant 0.18 isoniazid
kasA 2518702 c.588C>T synonymous_variant 0.35 isoniazid
kasA 2518711 c.597A>G synonymous_variant 0.32 isoniazid
kasA 2518714 c.600A>C synonymous_variant 0.29 isoniazid
kasA 2518717 c.603C>T synonymous_variant 0.27 isoniazid
kasA 2518747 c.633C>G synonymous_variant 0.26 isoniazid
ahpC 2726645 c.453C>G synonymous_variant 0.2 isoniazid
ahpC 2726657 c.465A>C synonymous_variant 0.2 isoniazid Not assoc w R - Interim
ahpC 2726669 p.Asp159Glu missense_variant 0.21 isoniazid
ahpC 2726672 c.480G>A synonymous_variant 0.18 isoniazid Not assoc w R - Interim
ahpC 2726681 c.489A>G synonymous_variant 0.19 isoniazid
thyX 3067661 c.285C>G synonymous_variant 0.23 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625762 c.852A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625765 c.849C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625797 p.Val273Met missense_variant 0.28 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625806 c.808A>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625852 c.762A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625864 c.-954T>G upstream_gene_variant 0.36 rifampicin
bedaquiline
mtrB 3625876 c.738G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
bedaquiline
mtrA 3627252 p.Ala33Val missense_variant 0.85 rifampicin
bedaquiline
rpoA 3877542 c.966C>T synonymous_variant 0.26 rifampicin
rpoA 3877553 p.Glu319Gln missense_variant 0.31 rifampicin
rpoA 3877557 c.951C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3878436 c.72A>G synonymous_variant 0.27 rifampicin
clpC1 4038740 c.1965G>C synonymous_variant 0.22 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.19 pyrazinamide
clpC1 4038851 c.1854G>A synonymous_variant 0.35 pyrazinamide
clpC1 4039025 c.1680C>T synonymous_variant 0.76 pyrazinamide
clpC1 4039484 c.1221T>G synonymous_variant 0.37 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.2 pyrazinamide
clpC1 4039524 p.Phe394Tyr missense_variant 0.21 pyrazinamide
glpK 4138547 c.1209C>T synonymous_variant 0.36 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
glpK 4138568 c.1188A>G synonymous_variant 0.27 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138571 c.1185C>G synonymous_variant 0.24 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138583 c.1173G>C synonymous_variant 0.2 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138586 c.1170C>T synonymous_variant 0.23 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4240780 c.918T>C synonymous_variant 0.35 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.34 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.29 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247491 c.978G>C synonymous_variant 0.23 ethambutol
embB 4248277 c.1764G>C synonymous_variant 0.29 ethambutol
embB 4248902 p.Thr797Pro missense_variant 1.0 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
aftB 4269183 c.-347T>C upstream_gene_variant 0.23 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R