TB-Profiler result

Run: ERR2515662
Summary

Run ID: ERR2515662

Sample name:

Date: 20-10-2023 14:00:55

Number of reads: 946502

Percentage reads mapped: 96.78

Strain: lineage2.2.1

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide R pncA p.Arg140Pro (1.00)
Streptomycin R rrs n.888G>A (0.42)
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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.42 streptomycin
pncA 2288823 p.Arg140Pro missense_variant 1.0 pyrazinamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.29
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.29
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.36
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.37
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.36
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.33
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.35
rrs 1472678 n.833_834delTTinsGCC non_coding_transcript_exon_variant 0.34
rrs 1472684 n.839_845delGGGATCCinsA non_coding_transcript_exon_variant 0.34
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.33
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.34
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.36
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.38
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.42
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.43
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.39
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.39
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.37
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.24
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.2
rrs 1472826 n.981G>A non_coding_transcript_exon_variant 0.2
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.21
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.21
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.21
rrs 1472837 n.992_993insTTTG non_coding_transcript_exon_variant 0.2
rrs 1472841 n.996_1002delGGACGCGinsAC non_coding_transcript_exon_variant 0.21
rrs 1472858 n.1013_1014insA non_coding_transcript_exon_variant 0.19
rrs 1472861 n.1016G>C non_coding_transcript_exon_variant 0.18
rrs 1472867 n.1022T>C non_coding_transcript_exon_variant 0.19
rrs 1472869 n.1024_1025delGTinsTCGGG non_coding_transcript_exon_variant 0.2
rrs 1472873 n.1028C>A non_coding_transcript_exon_variant 0.19
rrs 1472875 n.1030T>A non_coding_transcript_exon_variant 0.2
rrs 1472876 n.1031G>A non_coding_transcript_exon_variant 0.18
rrs 1472877 n.1032T>A non_coding_transcript_exon_variant 0.19
rrs 1472880 n.1035_1036insA non_coding_transcript_exon_variant 0.19
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747167 p.Lys144Asn missense_variant 1.0
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0