TB-Profiler result

Run: ERR2514399
Summary

Run ID: ERR2514399

Sample name:

Date: 31-03-2023 20:18:44

Number of reads: 5167246

Percentage reads mapped: 99.34

Strain: lineage3

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
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
tlyA 1918139 p.Ala67Glu missense_variant 0.5 capreomycin
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 6233 p.Ala332Thr missense_variant 0.99
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 575265 c.-83C>T upstream_gene_variant 0.18
ccsA 620168 p.Ala93Val missense_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
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
fbiC 1304125 p.Val399Ile missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475008 n.1351C>A non_coding_transcript_exon_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103221 c.-179C>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169204 c.1407_1408delAA frameshift_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
kasA 2519089 c.975C>T synonymous_variant 0.33
eis 2715014 p.Arg107Cys missense_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067289 c.657C>T synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642225 p.Gln231Lys missense_variant 0.29
alr 3841013 c.408C>T synonymous_variant 0.18
embC 4240480 c.618G>T synonymous_variant 0.12
embC 4240512 p.Ser217Thr missense_variant 0.17
embC 4240564 p.Met234Ile missense_variant 0.22
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242530 p.Arg890* stop_gained 1.0
embC 4242641 p.Arg927Cys missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0