TB-Profiler result

Run: ERR046939
Summary

Run ID: ERR046939

Sample name:

Date: 31-03-2023 08:58:07

Number of reads: 7273991

Percentage reads mapped: 99.45

Strain: lineage3.1.2.2

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
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.2 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
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
gyrA 9611 c.2310C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.28
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
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.21
rrl 1475526 n.1869C>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.51
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 0.99
eis 2714366 p.Val323Leu missense_variant 0.17
eis 2715586 c.-254G>C upstream_gene_variant 0.29
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746186 c.1413G>C synonymous_variant 0.23
pepQ 2859381 c.1038C>G synonymous_variant 0.18
ribD 2987307 p.Ala157Pro missense_variant 0.17
Rv2752c 3064741 p.Gly484Ala missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087476 c.657C>T synonymous_variant 1.0
fbiD 3339153 p.Leu12Phe missense_variant 0.15
fbiD 3339550 p.Gly145Trp missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.28
fbiB 3641955 p.Gly141Arg missense_variant 0.22
fbiB 3642734 c.1200G>C synonymous_variant 0.23
alr 3840268 p.Thr385Pro missense_variant 0.25
rpoA 3878238 p.Asp90Glu missense_variant 0.14
ddn 3987013 p.Gly57Ala missense_variant 0.21
clpC1 4038857 c.1848C>A synonymous_variant 0.16
clpC1 4039932 p.Gly258Val missense_variant 0.26
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.15
embC 4242476 p.Pro872Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.34
embB 4248725 p.Ser738Ala missense_variant 0.24
ubiA 4269529 p.Ala102Gly missense_variant 0.16
ethA 4326176 p.Glu433Ala missense_variant 0.99
ethA 4327672 c.-199G>A upstream_gene_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0