TB-Profiler result

Run: ERR270805
Summary

Run ID: ERR270805

Sample name:

Date: 31-03-2023 23:27:39

Number of reads: 1660259

Percentage reads mapped: 99.26

Strain: lineage6.3.1

Drug-resistance: HR-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
lineage6 West-Africa 2 AFRI_1 RD702 0.98
lineage6.3 West-Africa 2 AFRI_1 RD702 0.98
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.97
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8303 c.1002C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491317 p.Pro179Ser missense_variant 0.17
fgd1 491668 p.Lys296Glu missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576658 c.1311G>C synonymous_variant 0.12
rpoB 760969 p.Ser388Leu missense_variant 1.0
rpoB 761723 p.Glu639Asp missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766352 p.Val995Ile missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777986 c.495C>A synonymous_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.97
atpE 1461251 c.207G>T synonymous_variant 0.95
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
tlyA 1918125 p.Trp62Cys missense_variant 0.29
tlyA 1918247 p.Arg103His missense_variant 0.15
ndh 2102694 p.Val117Ile missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.96
kasA 2518132 c.18C>T synonymous_variant 0.98
ahpC 2726338 p.Val49Gly missense_variant 0.35
folC 2746695 p.Ala302Ser missense_variant 0.15
pepQ 2859531 c.888C>T synonymous_variant 0.15
pepQ 2859893 c.526C>T synonymous_variant 0.14
Rv2752c 3064886 p.Ala436Thr missense_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.97
ald 3087322 p.Pro168Leu missense_variant 0.17
fbiD 3339273 c.156T>G synonymous_variant 0.23
Rv3083 3449781 c.1278G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642446 c.912C>T synonymous_variant 0.22
rpoA 3877696 p.Thr271Ile missense_variant 0.98
clpC1 4038857 c.1848C>A synonymous_variant 0.27
embC 4240671 p.Thr270Ile missense_variant 0.96
embC 4241843 p.Leu661Ile missense_variant 1.0
embC 4242422 p.Trp854Gly missense_variant 0.22
embC 4242425 p.Arg855Gly missense_variant 0.5
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
aftB 4268477 c.360C>T synonymous_variant 0.86
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.94
aftB 4269522 c.-686C>T upstream_gene_variant 0.93
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0