TB-Profiler result

Run: ERR4817313
Summary

Run ID: ERR4817313

Sample name:

Date: 01-04-2023 14:55:17

Number of reads: 5107823

Percentage reads mapped: 95.41

Strain: lineage4.2.1.1

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 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 0.3 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288957 p.Tyr95* stop_gained 1.0 pyrazinamide
ethA 4327409 p.His22Pro missense_variant 1.0 ethionamide
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
mshA 575833 c.486C>T synonymous_variant 1.0
mshA 576092 p.Pro249Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.98
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800973 c.165C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471755 n.-91C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.25
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.4
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.2
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.22
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.22
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.7
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.18
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.91
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.82
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.83
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.82
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.8
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.18
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.55
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.5
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.5
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.4
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.38
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.36
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.36
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.27
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.18
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.25
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.4
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.54
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.46
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.38
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.23
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.25
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.23
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.22
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.22
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.15
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.67
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.67
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.67
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.5
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.5
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.25
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.6
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.4
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449132 p.Leu210Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987092 p.Glu83Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246587 p.Gly25Ala missense_variant 1.0
embB 4247790 p.Ser426Asn missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407969 c.233dupC frameshift_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0