TB-Profiler result

Run: ERR2245288
Summary

Run ID: ERR2245288

Sample name:

Date: 31-03-2023 17:37:11

Number of reads: 3142679

Percentage reads mapped: 99.06

Strain: lineage3.1.1

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 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili 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
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 576108 p.Ala254Gly missense_variant 0.35
ccsA 619705 c.-186G>A upstream_gene_variant 0.12
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
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
rrs 1473283 n.1438T>A non_coding_transcript_exon_variant 0.13
rrl 1474877 n.1220G>A non_coding_transcript_exon_variant 0.18
rrl 1475357 n.1701delT non_coding_transcript_exon_variant 0.29
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.11
rpsA 1834662 p.Asp374Ala missense_variant 0.17
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 2169029 p.Asp528Glu missense_variant 0.22
PPE35 2170461 p.Gly51Glu missense_variant 0.96
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
pncA 2289905 c.-664T>C upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987012 c.174C>T synonymous_variant 1.0
Rv2752c 3064566 c.1626G>C synonymous_variant 0.31
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339377 p.Asp87Ala missense_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612701 p.Asp139Val missense_variant 0.12
fbiA 3640410 c.-133A>G upstream_gene_variant 0.1
alr 3841612 c.-193_-192insC upstream_gene_variant 0.14
rpoA 3878641 c.-134C>G upstream_gene_variant 0.33
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249612 c.3099C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0