TB-Profiler result

Run: ERR2124092
Summary

Run ID: ERR2124092

Sample name:

Date: 24-01-2024 12:40:17

Number of reads: 4251047

Percentage reads mapped: 98.63

Strain: lineage1.2.2.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide
Streptomycin R gid c.102delG (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 1.0
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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
gyrB 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.99
gyrA 8525 c.1224C>T synonymous_variant 0.99
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.29
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.43
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.46
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.47
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.41
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.39
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.35
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.36
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.35
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.35
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.34
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.34
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.33
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.15
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.14
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.14
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.52
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.14
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.56
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.65
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.63
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.28
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.25
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.19
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.17
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.22
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.23
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.3
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.3
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.3
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.3
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.36
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.35
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.37
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.37
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.31
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.32
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.31
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.31
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.28
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.28
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169987 c.621_625delCGGCT frameshift_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289171 p.Gly24Val missense_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.98
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040234 c.471C>A synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 0.97
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4326647 p.Tyr276Ser missense_variant 0.99
whiB6 4338203 p.Arg107Cys missense_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0