TB-Profiler result

Run: ERR046816
Summary

Run ID: ERR046816

Sample name:

Date: 31-03-2023 08:52:15

Number of reads: 12820911

Percentage reads mapped: 98.95

Strain: lineage3.1.2

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
lineage3.1.2 East-African-Indian CAS;CAS2 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
rpsL 781687 p.Lys43Arg missense_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
gyrB 5347 c.108G>C synonymous_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8377 p.Asp359Gly missense_variant 0.19
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.16
mshA 576751 p.Lys468Asn missense_variant 0.21
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 0.34
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.23
rpoC 767305 p.Tyr1312* stop_gained 0.17
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
Rv1258c 1406242 p.Ala367Thr missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.22
ndh 2102891 p.Phe51Ser missense_variant 0.24
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169379 p.Phe412Val missense_variant 0.18
PPE35 2169866 c.747G>C synonymous_variant 0.37
Rv1979c 2222557 p.Thr203Ser 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
pncA 2289801 c.-560C>T upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064552 p.Arg547Pro missense_variant 0.27
Rv2752c 3064741 p.Gly484Ala missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.23
fbiD 3339550 p.Gly145Trp missense_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.23
fbiB 3641955 p.Gly141Arg missense_variant 0.2
fbiB 3642772 p.Asp413Ala missense_variant 0.13
ddn 3987013 p.Gly57Ala missense_variant 0.2
clpC1 4038857 c.1848C>A synonymous_variant 0.15
clpC1 4039932 p.Gly258Val missense_variant 0.3
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242476 p.Pro872Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.3
embB 4248725 p.Ser738Ala missense_variant 0.19
aftB 4268594 c.243C>T synonymous_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.18
ethA 4327672 c.-199G>A upstream_gene_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0