TB-Profiler result

Run: ERR4821603

Summary

Run ID: ERR4821603

Sample name:

Date: 01-04-2023 17:20:45

Number of reads: 383526

Percentage reads mapped: 99.42

Strain: lineage3.1.1

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 0.99
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
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
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759929 c.123A>G synonymous_variant 0.22
rpoB 761738 p.Ile644Met missense_variant 0.14
rpoB 762312 p.Gly836Ser missense_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765138 p.Thr590Asn missense_variant 0.13
rpoC 765958 c.2589C>G synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775926 p.Leu852Pro missense_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303565 p.Gly212Ala missense_variant 0.22
fbiC 1304303 p.Arg458His missense_variant 0.17
fbiC 1304638 p.Arg570* stop_gained 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476735 n.3078G>T non_coding_transcript_exon_variant 0.29
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 2168644 p.Phe657Leu missense_variant 1.0
PPE35 2169739 p.Thr292Ala missense_variant 0.18
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
kasA 2519074 c.960C>T synonymous_variant 0.25
ahpC 2725918 c.-274delA upstream_gene_variant 0.15
ahpC 2726069 c.-124A>C upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746329 p.Arg424Trp missense_variant 0.18
pepQ 2859601 c.817delG frameshift_variant 0.15
pepQ 2860219 p.Gln67Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339626 p.His170Pro missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613095 c.22T>C synonymous_variant 0.17
fbiB 3642134 c.600G>A synonymous_variant 0.29
ddn 3986814 c.-30T>A upstream_gene_variant 0.22
clpC1 4038698 c.2007C>T synonymous_variant 0.13
panD 4044259 p.Ser8Leu missense_variant 0.11
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247266 c.753C>A synonymous_variant 0.15
embB 4247954 p.Pro481Ser missense_variant 0.18
ubiA 4269896 c.-63G>A upstream_gene_variant 0.1
ethR 4327300 c.-249G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407958 p.Ala82Glu missense_variant 1.0