TB-Profiler result

Run: ERR245793
Summary

Run ID: ERR245793

Sample name:

Date: 31-03-2023 18:21:11

Number of reads: 10900317

Percentage reads mapped: 98.92

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
gid 4407816 c.386delG frameshift_variant 0.99 streptomycin
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 8056 p.Arg252Leu missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759831 p.Thr9Pro missense_variant 0.24
rpoB 762249 p.Leu815Val missense_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.37
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417501 c.-154A>C upstream_gene_variant 0.27
atpE 1461019 c.-26C>A upstream_gene_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.19
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.19
fabG1 1673449 p.Thr4Pro missense_variant 0.37
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.37
ndh 2102891 p.Phe51Ser missense_variant 0.21
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.36
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
eis 2714366 p.Val323Leu missense_variant 0.16
eis 2715586 c.-254G>C upstream_gene_variant 0.67
ahpC 2725954 c.-239C>T upstream_gene_variant 0.35
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746186 c.1413G>C synonymous_variant 0.21
pepQ 2859381 c.1038C>G synonymous_variant 0.23
Rv2752c 3064741 p.Gly484Ala missense_variant 0.23
Rv2752c 3065008 p.Pro395Arg missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.27
Rv3236c 3611982 p.Ala379Pro missense_variant 0.52
fbiB 3641955 p.Gly141Arg missense_variant 0.21
fbiB 3642734 c.1200G>C synonymous_variant 0.22
ddn 3987013 p.Gly57Ala missense_variant 0.25
clpC1 4038857 c.1848C>A synonymous_variant 0.29
clpC1 4039363 p.Ala448Pro missense_variant 0.29
clpC1 4039932 p.Gly258Val missense_variant 0.35
embC 4240646 p.Phe262Val missense_variant 0.2
embC 4241056 c.1194C>G synonymous_variant 0.3
embC 4241429 p.Phe523Val missense_variant 0.48
embC 4241456 p.Ala532Pro missense_variant 0.52
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242476 p.Pro872Ala missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embC 4242822 p.Val987Gly missense_variant 0.41
embC 4242827 p.Leu989Val missense_variant 0.19
embB 4249504 p.Gln997His missense_variant 0.24
aftB 4268812 p.Ser9Ala missense_variant 0.23
ubiA 4269529 p.Ala102Gly missense_variant 0.17
ethA 4327672 c.-199G>A upstream_gene_variant 0.25
ethA 4328212 c.-740delC upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0