TB-Profiler result

Run: SRR5341407

Summary

Run ID: SRR5341407

Sample name:

Date: 18-08-2022 09:36:54

Number of reads: 2252974

Percentage reads mapped: 83.71

Strain: lineage3.1.2.1

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
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 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 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.26 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288848 c.393dupC frameshift_variant 0.11 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4326972 c.501delG frameshift_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
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 765915 p.Tyr849Ser missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416519 p.Leu277Phe missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.15
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.15
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.13
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.13
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.13
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.13
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.11
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.1
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.12
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.16
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.16
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.17
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.16
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.15
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.11
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.27
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.24
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.23
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.21
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.18
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.14
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.13
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.13
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.13
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.14
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.15
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.17
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.16
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.17
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.29
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.39
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.34
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.32
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
pncA 2288937 p.Ala102Val missense_variant 0.5
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
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