TB-Profiler result

Run: ERR040136
Summary

Run ID: ERR040136

Sample name:

Date: 31-03-2023 08:47:10

Number of reads: 20285072

Percentage reads mapped: 99.01

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 761106 p.Met434Leu missense_variant 0.22 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 0.63 rifampicin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 762249 p.Leu815Val missense_variant 0.19
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.41
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.24
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
atpE 1461019 c.-26C>A upstream_gene_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.24
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155682 p.Ala144Thr missense_variant 0.83
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.18
Rv2752c 3064741 p.Gly484Ala missense_variant 0.26
thyA 3073806 c.666C>G synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642098 c.564G>A synonymous_variant 1.0
fbiB 3642734 c.1200G>C synonymous_variant 0.22
alr 3840636 p.Pro262Gln missense_variant 1.0
rpoA 3878622 c.-115C>G upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.31
embC 4239842 c.-21C>A upstream_gene_variant 0.16
embC 4241056 c.1194C>G synonymous_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 0.99
embC 4242425 p.Arg855Gly missense_variant 0.22
embC 4242476 p.Pro872Ala missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embC 4242822 p.Val987Gly missense_variant 0.35
embA 4244375 c.1143C>G synonymous_variant 0.29
embA 4245883 p.Gly884Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.23
ethA 4326230 p.Asp415Gly missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0