TB-Profiler result

Run: SRR10808490
Summary

Run ID: SRR10808490

Sample name:

Date: 2024-04-16T00:40:38.254228

Number of reads: 2235346

Percentage reads mapped: 85.36

Median coverage: 71.0

Strain: lineage2.2.1.1

Spoligotype:

Drug-resistance: Sensitive

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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
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 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
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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
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 761027 c.1221A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761102 c.1296A>G synonymous_variant 0.12 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762149 c.2343G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762158 c.2352G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763792 p.Glu141Asp missense_variant 0.12 rifampicin
rpoC 764254 c.885G>C synonymous_variant 0.12 rifampicin
rpoC 767068 c.3699G>C synonymous_variant 0.13 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.12 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
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781301 c.-259C>T upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471931 n.87delA non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472019 n.174G>A non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472023 n.178G>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472042 n.197T>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472848 n.1003T>A non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.19 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 1474830 n.1173A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475061 n.1404C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475062 n.1405A>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476679 n.3022T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rpsA 1833694 c.153G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833697 c.156C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833709 c.168C>T synonymous_variant 0.13 pyrazinamide
rpsA 1833730 c.189C>T synonymous_variant 0.12 pyrazinamide
rpsA 1833734 p.Ala65Ser missense_variant 0.13 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834759 c.1218A>C synonymous_variant 0.12 pyrazinamide
rpsA 1834774 c.1233C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834776 p.Ala412Glu missense_variant 0.13 pyrazinamide
rpsA 1834780 c.1239A>G synonymous_variant 0.12 pyrazinamide
rpsA 1834786 c.1245A>G synonymous_variant 0.13 pyrazinamide
rpsA 1834792 c.1251G>C synonymous_variant 0.12 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 2155361 p.Thr251Ala missense_variant 1.0 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.99 amikacin Not assoc w R
kanamycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038519 p.Arg729Gln missense_variant 0.12 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039226 c.1479T>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4039241 c.1464G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039265 c.1440C>T synonymous_variant 0.12 pyrazinamide
clpC1 4040291 c.414G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040303 c.402G>C synonymous_variant 0.15 pyrazinamide
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 4248115 c.1602C>T synonymous_variant 0.91 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 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