TB-Profiler result

Run: ERR2179858
Summary

Run ID: ERR2179858

Sample name:

Date: 15-08-2022 11:57:28

Number of reads: 1323248

Percentage reads mapped: 72.32

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 0.98
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 1918524 c.589delG frameshift_variant 0.22 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 5878 c.639G>T synonymous_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9385 p.Arg695His missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620187 c.297C>T synonymous_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 767229 p.Ser1287Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777451 p.Val344Ile missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303377 p.Asp149Glu missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475658 n.2001G>A non_coding_transcript_exon_variant 0.13
ndh 2102038 c.1004delG frameshift_variant 0.15
ndh 2102233 c.810G>A synonymous_variant 1.0
ndh 2102875 c.168C>T synonymous_variant 0.18
katG 2155588 p.Ser175Leu missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 0.94
Rv1979c 2221992 c.1173C>A synonymous_variant 0.13
Rv1979c 2222024 p.Ala381Thr missense_variant 0.18
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 2289651 c.-410T>C upstream_gene_variant 0.17
pncA 2289909 c.-668G>A upstream_gene_variant 0.15
eis 2714318 p.Arg339Trp missense_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747168 p.Lys144Thr missense_variant 0.13
ribD 2987503 p.Gly222Asp missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087096 p.Thr93Ala missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474684 p.Asp226Glu missense_variant 0.18
fprA 3474842 p.Lys279Thr missense_variant 0.15
Rv3236c 3612074 p.Ile348Thr missense_variant 0.12
fbiB 3641400 c.-135C>T upstream_gene_variant 0.17
rpoA 3877797 c.711G>A synonymous_variant 0.12
clpC1 4038634 p.Glu691* stop_gained 0.2
clpC1 4040753 c.-49G>A upstream_gene_variant 1.0
embC 4239870 p.Thr3Ile missense_variant 0.13
embC 4241231 p.Arg457Trp missense_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4243545 p.Leu105Met missense_variant 0.14
embB 4246268 c.-246G>A upstream_gene_variant 0.13
aftB 4268511 p.Ser109Asn missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0