TB-Profiler result

Run: ERR025892
Summary

Run ID: ERR025892

Sample name:

Date: 31-03-2023 08:19:14

Number of reads: 883441

Percentage reads mapped: 33.0

Strain: lineage6.1.3

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
lineage6 West-Africa 2 AFRI_1 RD702 0.99
lineage6.1.3 West-Africa 2 AFRI_1 RD702 0.98
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
embC 4240781 p.Ala307Thr missense_variant 0.71 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
gyrB 6446 p.Ala403Ser missense_variant 0.95
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8493 p.Leu398Phe missense_variant 1.0
gyrA 8806 p.Asp502Gly missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.25
fgd1 491668 p.Lys296Glu missense_variant 0.88
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576520 c.1173C>T synonymous_variant 0.25
ccsA 620410 p.Ile174Leu missense_variant 0.44
rpoB 760855 p.Thr350Ile missense_variant 1.0
rpoB 760969 p.Ser388Leu missense_variant 1.0
rpoB 761723 p.Glu639Asp missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.91
rpoC 766231 c.2862T>C synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406141 c.1200G>A synonymous_variant 1.0
Rv1258c 1406685 p.Val219Ala missense_variant 0.83
embR 1416633 p.Leu239Val missense_variant 1.0
atpE 1461251 c.207G>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674434 p.Val78Ala missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.82
katG 2155503 c.609C>T synonymous_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169318 p.Phe432Cys missense_variant 0.2
PPE35 2169320 p.Leu431Phe missense_variant 0.22
PPE35 2169379 p.Phe412Val missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.9
thyA 3073806 c.666C>G synonymous_variant 0.4
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087544 p.Pro242Leu missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612143 p.Arg325His missense_variant 1.0
alr 3840268 p.Thr385Pro missense_variant 0.5
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241843 p.Leu661Ile missense_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244379 p.Pro383Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249429 c.2916C>G synonymous_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269522 c.-686C>T upstream_gene_variant 0.83
ubiA 4269529 p.Ala102Gly missense_variant 0.35
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 0.93
ethR 4327909 p.Thr121Pro missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338602 c.-81A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.83
gid 4408034 p.Glu57Lys missense_variant 1.0