TB-Profiler result

Run: ERR4818306
Summary

Run ID: ERR4818306

Sample name:

Date: 01-04-2023 15:29:06

Number of reads: 628101

Percentage reads mapped: 99.63

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
tlyA 1918503 c.567delA frameshift_variant 0.12 capreomycin
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
gyrB 5224 c.-15_-12delGAGA upstream_gene_variant 0.14
gyrB 6276 p.Thr346Ile missense_variant 1.0
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 490717 c.-66C>T upstream_gene_variant 1.0
fgd1 490738 c.-45C>G upstream_gene_variant 0.17
fgd1 491383 p.Glu201* stop_gained 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Gly missense_variant 0.1
mshA 576226 c.879G>C synonymous_variant 0.11
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761501 c.1698delC frameshift_variant 0.18
rpoB 761671 p.Thr622Ile missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762505 p.Phe900Ser missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764889 p.Leu507Ser missense_variant 0.13
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
fbiC 1303485 c.555C>A synonymous_variant 0.15
fbiC 1303776 p.Lys282Asn missense_variant 0.15
fbiC 1303851 c.921C>T synonymous_variant 0.2
fbiC 1303854 c.924T>C synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918474 p.Pro179Ala missense_variant 0.12
katG 2153949 c.2163G>C synonymous_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155622 p.Leu164Met missense_variant 0.11
PPE35 2167869 p.Gly915Val missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168685 p.Thr643Asn missense_variant 0.18
Rv1979c 2222201 p.Gly322Arg missense_variant 0.18
Rv1979c 2222265 p.Phe300Leu missense_variant 0.17
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 2289433 c.-192C>T upstream_gene_variant 0.13
eis 2714498 c.834delG frameshift_variant 0.22
eis 2715265 p.Ser23Thr missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859342 c.1077G>A synonymous_variant 0.13
pepQ 2860219 p.Gln67Leu missense_variant 0.17
thyX 3067999 c.-54G>C upstream_gene_variant 0.1
thyA 3074418 c.54A>G synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087254 c.435C>T synonymous_variant 0.29
Rv3083 3449820 c.1317G>T synonymous_variant 0.25
fprA 3473820 c.-187C>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612998 p.Gly40Asp missense_variant 0.15
Rv3236c 3613137 c.-22delA upstream_gene_variant 0.15
fbiB 3642517 p.Ala328Asp missense_variant 0.11
fbiB 3642830 c.1296G>A synonymous_variant 1.0
alr 3840672 p.Leu250Pro missense_variant 0.17
clpC1 4040626 p.Tyr27His missense_variant 0.14
embC 4239720 c.-142_-141delCC upstream_gene_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245234 c.2003delT frameshift_variant 0.11
aftB 4268352 c.482_484delCGC disruptive_inframe_deletion 0.15
ubiA 4269307 p.Phe176Ser missense_variant 0.14
ethA 4326958 p.Asp172Glu missense_variant 0.29
ethR 4327858 p.Arg104Ser missense_variant 0.2
ethA 4328417 c.-944G>T upstream_gene_variant 0.11
ethA 4328457 c.-984C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0