TB-Profiler result

Run: ERR2679289
Summary

Run ID: ERR2679289

Sample name:

Date: 31-03-2023 23:01:19

Number of reads: 522547

Percentage reads mapped: 99.59

Strain: lineage6.2.3;lineage4.1.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 0.86
lineage6.2 West-Africa 2 AFRI_1 RD702 0.09
lineage4.1 Euro-American T;X;H None 0.8
lineage4.1.2 Euro-American T;H None 0.7
lineage6.2.3 West-Africa 2 AFRI_1 RD702 0.21
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.73
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
katG 2155168 p.Ser315Thr missense_variant 0.85 isoniazid
gid 4407851 c.351delG frameshift_variant 0.71 streptomycin
gid 4407967 p.Leu79Ser missense_variant 0.16 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
gyrB 5072 c.-168G>T upstream_gene_variant 0.12
gyrB 6446 p.Ala403Ser missense_variant 0.15
gyrB 7121 p.Pro628Ser missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8478 p.Gly393Ser missense_variant 0.72
gyrA 8493 p.Leu398Phe missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.85
fgd1 491668 p.Lys296Glu missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 0.16
mshA 575679 p.Asn111Ser missense_variant 0.71
rpoB 759989 c.183G>A synonymous_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 0.76
rpoB 761723 p.Glu639Asp missense_variant 0.32
rpoC 765150 p.Gly594Glu missense_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.35
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406685 p.Val219Ala missense_variant 0.25
atpE 1461251 c.207G>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674434 p.Val78Ala missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.23
katG 2155503 c.609C>T synonymous_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.19
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.64
kasA 2518132 c.18C>T synonymous_variant 0.13
ald 3086728 c.-92C>T upstream_gene_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.18
alr 3840559 p.Arg288Ser missense_variant 0.23
alr 3840618 p.Asp268Gly missense_variant 0.21
clpC1 4038408 p.Pro766Leu missense_variant 0.72
embC 4240671 p.Thr270Ile missense_variant 0.23
embC 4241843 p.Leu661Ile missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.92
embA 4243541 c.309C>T synonymous_variant 0.36
embA 4244220 c.988C>T synonymous_variant 0.26
embA 4244379 p.Pro383Ser missense_variant 0.32
embA 4246087 p.Gln952Arg missense_variant 0.11
embB 4246864 c.351C>T synonymous_variant 0.19
embB 4247646 p.Glu378Ala missense_variant 0.17
aftB 4269351 c.-515C>T upstream_gene_variant 0.27
ubiA 4269387 p.Glu149Asp missense_variant 0.29
aftB 4269522 c.-686C>T upstream_gene_variant 0.22
aftB 4269606 c.-770T>C upstream_gene_variant 0.17
ubiA 4269719 p.Ala39Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.15
gid 4408437 c.-235T>A upstream_gene_variant 0.11