TB-Profiler result

Run: ERR4799323

Summary

Run ID: ERR4799323

Sample name:

Date: 01-04-2023 09:02:12

Number of reads: 3026702

Percentage reads mapped: 99.68

Strain: lineage3.1.2.1

Drug-resistance: Sensitive


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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 0.98
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.9
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.96
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.93
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
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 0.98
gyrA 9304 p.Gly668Asp missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.98
rpoC 762434 c.-936T>G upstream_gene_variant 0.98
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475372 n.1715A>G non_coding_transcript_exon_variant 0.11
rrl 1475433 n.1776A>G non_coding_transcript_exon_variant 0.13
rrl 1475475 n.1818C>A non_coding_transcript_exon_variant 0.13
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.11
rrl 1476092 n.2435A>G non_coding_transcript_exon_variant 0.11
rrl 1476152 n.2495T>C 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 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.95
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.96