TB-Profiler result

Run: SRR7645936
Summary

Run ID: SRR7645936

Sample name:

Date: 2024-04-14T03:59:59.878008

Number of reads: 1271178

Percentage reads mapped: 23.37

Median coverage: 22.0

Strain: lineage2.2.1

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 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 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
Rv0565c 657370 p.Gln34Arg missense_variant 1.0 ethionamide Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 762911 p.Ile1035Met missense_variant 0.43 rifampicin
rpoB 762920 c.3114C>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.42 rifampicin
rpoB 762942 c.3136_3138delATCinsGG frameshift_variant&missense_variant 0.44 rifampicin
rpoC 762947 c.-423C>G upstream_gene_variant 0.41 rifampicin
rpoB 762968 c.3162G>A synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 762971 c.-399G>C upstream_gene_variant 0.48 rifampicin
rpoC 764618 c.1249C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764623 c.1254C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764665 c.1296C>G synonymous_variant 0.48 rifampicin
rpoC 764668 c.1299C>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764671 c.1302G>A synonymous_variant 0.5 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764680 c.1311G>A synonymous_variant 0.5 rifampicin
rpoC 764701 c.1332C>G synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 766645 p.Glu1092Asp missense_variant 1.0 rifampicin Not assoc w R
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 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
sigE 1364706 c.294G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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 1472164 n.319G>A non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.82 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.87 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.78 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.64 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.62 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472709 n.864T>G non_coding_transcript_exon_variant 0.61 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.66 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.66 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.89 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.89 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.77 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.34 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.62 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.72 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474494 n.837C>G non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474495 n.838G>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474503 n.846G>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1474509 n.852G>C non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1474528 n.871T>A non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1474530 n.873G>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474539 n.882C>A non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1474573 n.916C>T non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1474576 n.919T>A non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474586 n.929T>A non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474587 n.930G>A non_coding_transcript_exon_variant 0.63 capreomycin
linezolid
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.81 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.57 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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
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
Rv2752c 3064731 p.Leu487Phe missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
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
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
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 0.95 streptomycin Not assoc w R