TB-Profiler result

Run: ERR046982
Summary

Run ID: ERR046982

Sample name:

Date: 31-03-2023 08:59:49

Number of reads: 4532062

Percentage reads mapped: 99.5

Strain: lineage3.1.1

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
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
gid 4407851 c.351delG frameshift_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575932 p.Glu195Asp missense_variant 0.24
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.26
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.19
mmpR5 779371 p.Ala128Pro missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.35
inhA 1674892 p.Asn231Asp missense_variant 0.35
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 2169866 c.747G>C synonymous_variant 0.4
PPE35 2170367 c.246G>A synonymous_variant 1.0
PPE35 2170461 p.Gly51Glu missense_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
eis 2714366 p.Val323Leu missense_variant 0.3
eis 2715586 c.-254G>C upstream_gene_variant 0.4
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064741 p.Gly484Ala missense_variant 0.37
thyX 3067995 c.-50A>C upstream_gene_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339550 p.Gly145Trp missense_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.33
fbiB 3641955 p.Gly141Arg missense_variant 0.19
fbiB 3642734 c.1200G>C synonymous_variant 0.27
fbiB 3642772 p.Asp413Ala missense_variant 0.33
alr 3840268 p.Thr385Pro missense_variant 0.37
clpC1 4038857 c.1848C>A synonymous_variant 0.16
clpC1 4039932 p.Gly258Val missense_variant 0.3
embC 4239842 c.-21C>A upstream_gene_variant 0.13
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242476 p.Pro872Ala missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.44
embC 4242827 p.Leu989Val missense_variant 0.24
ubiA 4269529 p.Ala102Gly missense_variant 0.2
ethA 4327672 c.-199G>A upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0