TB-Profiler result

Run: ERR2514873
Summary

Run ID: ERR2514873

Sample name:

Date: 31-03-2023 20:36:57

Number of reads: 740519

Percentage reads mapped: 95.16

Strain: lineage3

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
lineage3 East-African-Indian CAS 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
katG 2155182 c.929delA frameshift_variant 0.12 isoniazid
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
gyrB 6459 p.Val407Ala missense_variant 0.15
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 759620 c.-187A>C upstream_gene_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762380 c.-990T>G upstream_gene_variant 0.2
rpoC 762395 c.-975G>C upstream_gene_variant 0.14
rpoC 762398 c.-972T>C upstream_gene_variant 0.14
rpoC 762401 c.-969G>C upstream_gene_variant 0.12
rpoC 762404 c.-966T>C upstream_gene_variant 0.13
rpoC 762410 c.-960T>C upstream_gene_variant 0.13
rpoC 762416 c.-954A>G upstream_gene_variant 0.13
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765144 c.1779delC frameshift_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777122 c.1359C>T synonymous_variant 0.11
mmpL5 777128 c.1353A>G synonymous_variant 0.11
mmpS5 778508 p.Ala133Val missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303323 c.393T>G synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472937 n.1092A>G non_coding_transcript_exon_variant 1.0
rrl 1476668 n.3011C>T non_coding_transcript_exon_variant 0.22
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 2167965 p.Ala883Gly missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746745 p.Val285Gly missense_variant 0.5
Rv2752c 3065542 p.Glu217Gly missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448877 p.Thr125Ile missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249627 c.3114G>A synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0