TB-Profiler result

Run: ERR11050074
Summary

Run ID: ERR11050074

Sample name:

Date: 02-04-2023 10:31:15

Number of reads: 2889165

Percentage reads mapped: 99.41

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 4407967 p.Leu79Ser 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
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 9596 c.2295G>T synonymous_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.19
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576110 p.Ala255Pro missense_variant 0.29
mshA 576113 p.Arg256Gly missense_variant 0.6
mshA 576606 p.Ala420Gly missense_variant 0.28
mshA 576613 c.1266A>C synonymous_variant 0.33
mshA 576616 c.1269G>C synonymous_variant 0.43
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761161 p.Leu452Arg missense_variant 0.21
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762957 c.-413C>T upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.23
rpoC 764537 p.Pro390Ala missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.23
fabG1 1673553 p.Asp38Glu missense_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102275 c.768C>T synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170037 c.576C>G synonymous_variant 0.2
PPE35 2170386 p.Leu76Arg missense_variant 0.18
PPE35 2170390 p.Trp75Gly missense_variant 0.19
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
kasA 2519071 p.Asp319Glu missense_variant 0.33
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747792 c.-194G>T upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339751 p.Ala212Pro missense_variant 0.44
Rv3083 3449066 c.565delG frameshift_variant 1.0
Rv3083 3449260 p.Lys253* stop_gained 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474213 p.Lys69Asn missense_variant 0.19
whiB7 3568428 c.252A>G synonymous_variant 0.67
whiB7 3568431 c.249C>G synonymous_variant 0.67
Rv3236c 3613261 c.-145T>G upstream_gene_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.7
clpC1 4040550 p.Leu52Trp missense_variant 0.2
panD 4044291 c.-10G>A upstream_gene_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243682 c.450T>G synonymous_variant 0.19
embB 4246527 p.Ala5Gly missense_variant 0.55
embB 4247016 p.Ser168Trp missense_variant 0.21
embB 4247020 c.507C>G synonymous_variant 0.21
embB 4248328 c.1815G>C synonymous_variant 0.17
whiB6 4338200 p.Asp108His missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0