TB-Profiler result

Run: ERR040123
Summary

Run ID: ERR040123

Sample name:

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

Number of reads: 19653825

Percentage reads mapped: 99.15

Strain: lineage3.1.2.1

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
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 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 761154 p.Ser450Gln missense_variant 0.96 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288933 p.Tyr103* stop_gained 0.11 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4327054 p.Tyr140* stop_gained 0.17 ethionamide
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 0.99
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762249 p.Leu815Val missense_variant 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.34
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.17
rpoC 767305 p.Tyr1312* stop_gained 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18
inhA 1674952 p.Pro251Ala missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.99
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.2
eis 2714460 c.873G>A synonymous_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.22
pepQ 2859974 p.Ala149Pro missense_variant 0.18
Rv2752c 3064552 p.Arg547Pro missense_variant 0.22
Rv2752c 3067141 c.-951delC upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.23
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 0.22
clpC1 4038857 c.1848C>A synonymous_variant 0.16
clpC1 4039932 p.Gly258Val missense_variant 0.25
embC 4241056 c.1194C>G synonymous_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.16
embC 4242476 p.Pro872Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.32
ubiA 4269271 p.Val188Ala missense_variant 0.11
ubiA 4269311 p.Trp175Gly missense_variant 0.21
ubiA 4269529 p.Ala102Gly missense_variant 0.22
ethA 4327672 c.-199G>A upstream_gene_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407657 c.545delG frameshift_variant 1.0