TB-Profiler result

Run: ERR773806
Summary

Run ID: ERR773806

Sample name:

Date: 2024-04-15T16:42:43.814925

Number of reads: 850247

Percentage reads mapped: 21.52

Median coverage: 17.0

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 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
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
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 762863 c.3057T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762872 p.Met1022Ile missense_variant 0.44 rifampicin Uncertain significance
rpoB 762878 p.Ile1024Met missense_variant 0.46 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 0.46 rifampicin Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.71 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoB 762939 c.3133_3135delATGinsCC frameshift_variant&missense_variant 0.69 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.69 rifampicin Uncertain significance
rpoC 762980 c.-390T>C upstream_gene_variant 0.51 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.51 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.52 rifampicin
rpoC 762998 c.-372G>A upstream_gene_variant 0.42 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764410 c.1041G>C synonymous_variant 0.38 rifampicin
rpoC 764419 c.1050C>G synonymous_variant 0.47 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.49 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066_1068delAGGinsCC frameshift_variant&missense_variant 0.49 rifampicin
rpoC 764446 p.Asp359Glu missense_variant 0.51 rifampicin
rpoC 764450 c.1081_1083delGGTinsCC frameshift_variant&missense_variant 0.51 rifampicin
rpoC 764461 p.Glu364Asp missense_variant 0.53 rifampicin
rpoC 764468 p.Val367Ile missense_variant 0.53 rifampicin
rpoC 764471 p.Asn368Arg missense_variant 0.55 rifampicin
rpoC 764479 c.1110G>A synonymous_variant 0.53 rifampicin
rpoC 764503 c.1134G>C synonymous_variant 0.54 rifampicin
rpoC 764509 c.1140G>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764660 p.Val431Thr missense_variant 0.39 rifampicin
rpoC 764665 c.1296C>G synonymous_variant 0.38 rifampicin
rpoC 764671 c.1302G>C synonymous_variant 0.38 rifampicin
rpoC 764672 p.Gln435Glu missense_variant 0.39 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764687 p.Gln440Glu missense_variant 0.38 rifampicin
rpoC 764695 c.1326T>C synonymous_variant 0.41 rifampicin
rpoC 764705 p.Leu446Lys missense_variant 0.39 rifampicin
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 0.96 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471877 n.32A>G non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471893 n.48T>G non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.62 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.68 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.68 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.72 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.71 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.63 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.78 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 0.78 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 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.58 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474838 n.1181C>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1474893 n.1236G>A non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474899 n.1242T>C non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474910 n.1253C>G non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475499 n.1842C>G non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1475526 n.1869C>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475553 n.1896G>C non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475571 n.1914A>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475575 n.1918C>A non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1475577 n.1920C>G non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.43 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476279 n.2622G>C non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.65 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 1476339 n.2682G>A non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.63 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.59 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rpsA 1833254 c.-288G>C upstream_gene_variant 1.0 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.89 pyrazinamide Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.9 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
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
fbiA 3641332 p.Gly264Arg missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
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 1.0 streptomycin Not assoc w R