TB-Profiler result

Run: ERR2510602
Summary

Run ID: ERR2510602

Sample name:

Date: 31-03-2023 18:50:05

Number of reads: 980610

Percentage reads mapped: 99.38

Strain: lineage3

Drug-resistance: MDR-TB

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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
rpoB 761110 p.Asp435Gly missense_variant 0.96 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407760 p.Trp148* stop_gained 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
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620320 p.Pro144Ser missense_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
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
mmpL5 777721 p.Arg254Trp missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304907 c.1977C>T synonymous_variant 0.73
Rv1258c 1406236 p.Pro369Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834240 c.699T>A synonymous_variant 0.11
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 2170048 p.Leu189Val missense_variant 0.1
PPE35 2170053 p.Thr187Ser missense_variant 0.1
Rv1979c 2222313 c.852G>A synonymous_variant 0.14
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 2518298 p.Gly62Ser missense_variant 0.14
kasA 2519179 c.1065G>A synonymous_variant 0.14
kasA 2519190 p.Val359Glu missense_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747538 p.Pro21Ser missense_variant 1.0
thyX 3067266 c.678_679dupGT frameshift_variant 0.12
thyX 3067829 c.117C>A synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339719 p.Leu201His missense_variant 0.22
Rv3083 3448554 p.Ile17Met missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474086 p.Asp27Gly missense_variant 0.1
fprA 3475096 p.Pro364Ser missense_variant 1.0
whiB7 3568688 c.-10delG upstream_gene_variant 0.12
fbiB 3642407 c.873C>T synonymous_variant 0.14
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242636 p.Ala925Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267027 p.Arg604Cys missense_variant 0.12
aftB 4268329 p.Met170Leu missense_variant 0.11
ubiA 4268990 p.Arg282Trp missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0