TB-Profiler result

Run: ERR2514106
Summary

Run ID: ERR2514106

Sample name:

Date: 31-03-2023 20:07:28

Number of reads: 1910092

Percentage reads mapped: 98.97

Strain: lineage3

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 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
gyrA 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764931 p.Ala521Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.13
mmpL5 777122 c.1359C>T synonymous_variant 0.13
mmpL5 777128 c.1353A>G synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.15
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.14
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.14
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.23
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.15
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.32
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.32
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.11
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.24
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.13
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.38
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.27
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.24
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.44
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.29
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.29
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.18
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.3
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.3
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.33
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.5
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.5
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.7
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.44
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.44
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.33
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.33
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.33
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.33
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.38
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.33
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.33
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.33
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.33
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.27
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrl 1473769 n.112T>A non_coding_transcript_exon_variant 0.14
rrl 1475133 n.1479delG non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.3
rrl 1476561 n.2904C>T non_coding_transcript_exon_variant 0.9
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 2222038 p.Gly376Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>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
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407967 p.Leu79Trp missense_variant 1.0