TB-Profiler result

Run: SRR069981
Summary

Run ID: SRR069981

Sample name:

Date: 2024-04-16T05:25:24.430972

Number of reads: 1402019

Percentage reads mapped: 76.21

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 0.98
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.98
lineage2.2 East-Asian (Beijing) RD105;RD207 0.8
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 embB p.His312Arg Mutation from literature
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
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 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance Mutation from literature
katG 2155108 c.1002_1003dupGA frameshift_variant 0.95 isoniazid Assoc w R High-level resistance
kasA 2518310 p.Asp66Asn missense_variant 1.0 isoniazid Mutation from literature
embB 4247448 p.His312Arg missense_variant 0.2 ethambutol 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 8294 c.993T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8324 c.1023T>C synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8399 c.1098T>C synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9200 c.1899A>G synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9204 p.Ser635Thr missense_variant 0.29 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490842 c.60C>G synonymous_variant 0.24 clofazimine
pretomanid
delamanid
fgd1 491583 c.801G>A synonymous_variant 0.26 clofazimine
pretomanid
delamanid
fgd1 491595 c.813C>G synonymous_variant 0.22 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
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
hadA 731774 c.-156T>C upstream_gene_variant 0.33 isoniazid
nusG 734532 c.279A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760418 c.612G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760591 p.Val262Ala missense_variant 0.29 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 760970 c.1164G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763456 c.87A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763633 c.264T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.23 rifampicin
rpoC 764131 c.762T>C synonymous_variant 0.23 rifampicin
rpoC 764161 c.792G>C synonymous_variant 0.23 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764206 c.837T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764266 c.897T>C synonymous_variant 0.27 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.25 rifampicin
rpoC 764695 c.1326T>C synonymous_variant 0.18 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765613 p.His748Gln missense_variant 0.3 rifampicin
rpoC 765625 c.2256C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765628 c.2259G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 765631 p.Asp754Glu missense_variant 0.27 rifampicin
rpoC 765658 c.2289C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 765700 c.2331T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765751 c.2382C>G synonymous_variant 0.16 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.16 rifampicin Uncertain significance
rpoC 765892 c.2523T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 766549 c.3180G>C synonymous_variant 0.29 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.24 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781608 c.49_51delAGTinsGC frameshift_variant&missense_variant 0.26 streptomycin Uncertain significance
rpsL 781631 c.72G>C synonymous_variant 0.34 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.32 streptomycin Uncertain significance
rplC 800612 c.-197A>G upstream_gene_variant 0.19 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304574 c.1644C>G synonymous_variant 0.23 clofazimine
pretomanid
delamanid
fbiC 1304580 c.1650T>C synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fbiC 1304946 c.2016G>C synonymous_variant 0.36 clofazimine
pretomanid
delamanid
fbiC 1304958 c.2028T>G synonymous_variant 0.35 clofazimine
pretomanid
delamanid
atpE 1461219 c.175T>C synonymous_variant 0.27 bedaquiline
atpE 1461224 c.180T>C synonymous_variant 0.28 bedaquiline
atpE 1461233 c.189A>G synonymous_variant 0.27 bedaquiline
atpE 1461254 c.210T>C synonymous_variant 0.21 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474112 n.455T>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833619 c.78A>C synonymous_variant 0.18 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.22 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834261 c.720A>C synonymous_variant 0.24 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834297 c.756C>G synonymous_variant 0.4 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.38 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.38 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>A synonymous_variant 0.28 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.3 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834558 c.1017C>G synonymous_variant 0.26 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834666 c.1125G>C synonymous_variant 0.3 pyrazinamide
rpsA 1834669 c.1128G>C synonymous_variant 0.34 pyrazinamide
rpsA 1834688 c.1147_1149delAGTinsTCC synonymous_variant 0.23 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
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155632 c.480A>C synonymous_variant 0.28 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.28 isoniazid
katG 2155641 p.Lys157Asn missense_variant 0.26 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.95 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783158 c.885A>G synonymous_variant 0.25 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783971 c.72G>C synonymous_variant 0.22 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783980 c.63C>G synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783992 c.51T>C synonymous_variant 0.26 ethambutol Not assoc w R - Interim
moxifloxacin
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
Rv2752c 3066087 c.105A>G synonymous_variant 0.28 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyA 3073989 c.483T>C synonymous_variant 0.21 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
lpqB 3624464 c.447A>G synonymous_variant 0.28 bedaquiline
rifampicin
lpqB 3624470 c.441T>C synonymous_variant 0.26 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627252 p.Ala33Val missense_variant 0.91 bedaquiline
rifampicin
rpoA 3877557 c.951C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877613 p.Ile299Val missense_variant 0.38 rifampicin
rpoA 3877638 c.870T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877656 c.852T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoA 3877962 c.546G>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877986 c.522G>C synonymous_variant 0.32 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.25 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.24 rifampicin
clpC1 4038596 c.2109A>G synonymous_variant 0.2 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.35 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.33 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
clpC1 4039025 c.1680C>T synonymous_variant 0.81 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.23 pyrazinamide
clpC1 4040036 c.669C>G synonymous_variant 0.23 pyrazinamide
panD 4045034 c.-753A>T upstream_gene_variant 0.19 pyrazinamide
glpK 4139630 c.126C>T synonymous_variant 0.26 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247440 c.927C>G synonymous_variant 0.19 ethambutol
embB 4247470 c.957T>C synonymous_variant 0.15 ethambutol
embB 4247491 c.978G>C synonymous_variant 0.2 ethambutol
embB 4248220 c.1707A>G synonymous_variant 0.21 ethambutol Not assoc w R - Interim
embB 4248902 p.Thr797Pro missense_variant 1.0 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.83 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
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