TB-Profiler result

Run: ERR4815341
Summary

Run ID: ERR4815341

Sample name:

Date: 01-04-2023 13:48:46

Number of reads: 2330535

Percentage reads mapped: 99.35

Strain: lineage3.1.2.1

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
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 0.99
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 0.33 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
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 576751 p.Lys468Asn missense_variant 0.26
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 766479 p.Ala1037Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775946 c.2535C>T synonymous_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777053 c.1428G>A synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.14
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.14
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.25
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.27
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.17
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.17
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.17
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.25
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.29
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.25
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.2
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.31
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.31
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.12
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.11
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.1
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.1
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.22
rrl 1476087 n.2430C>T non_coding_transcript_exon_variant 0.25
rrl 1476405 n.2748C>T non_coding_transcript_exon_variant 0.14
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 2168604 p.Pro670Leu 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
Rv3236c 3612529 c.588C>T synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267885 p.Ser318Gly missense_variant 1.0
whiB6 4338594 c.-73T>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99