TB-Profiler result

Run: ERR9786868
Summary

Run ID: ERR9786868

Sample name:

Date: 02-04-2023 12:49:08

Number of reads: 2987498

Percentage reads mapped: 99.72

Strain: lineage6.1.3;lineage4.3.4.2

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
lineage4 Euro-American LAM;T;S;X;H None 0.78
lineage6 West-Africa 2 AFRI_1 RD702 0.25
lineage4.3 Euro-American (LAM) mainly-LAM None 0.77
lineage6.1.3 West-Africa 2 AFRI_1 RD702 0.25
lineage4.3.4 Euro-American (LAM) LAM RD174 0.78
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.76
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 0.31 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 0.22
gyrA 6817 c.-485G>A upstream_gene_variant 0.77
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8493 p.Leu398Phe missense_variant 0.29
gyrA 8806 p.Asp502Gly missense_variant 0.25
gyrA 9143 c.1842T>C synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491668 p.Lys296Glu missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 0.25
rpoB 760855 p.Thr350Ile missense_variant 0.26
rpoB 760969 p.Ser388Leu missense_variant 0.21
rpoB 761723 p.Glu639Asp missense_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 0.78
rpoC 766231 c.2862T>C synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.22
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.17
Rv1258c 1406685 p.Val219Ala missense_variant 0.23
embR 1416633 p.Leu239Val missense_variant 0.25
atpE 1461251 c.207G>T synonymous_variant 0.26
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.25
rrl 1473633 n.-25C>T upstream_gene_variant 0.22
inhA 1674434 p.Val78Ala missense_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.28
katG 2155503 c.609C>T synonymous_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 0.28
Rv1979c 2222308 p.Asp286Gly missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.21
eis 2714432 p.Val301Ile missense_variant 0.8
thyA 3073868 p.Thr202Ala missense_variant 0.74
ald 3086728 c.-92C>T upstream_gene_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.22
ald 3087412 p.Asp198Val missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.26
Rv3236c 3612009 p.Ala370Thr missense_variant 0.8
Rv3236c 3612143 p.Arg325His missense_variant 0.18
rpoA 3877740 c.768G>C synonymous_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 0.73
embC 4239763 c.-100C>T upstream_gene_variant 0.76
embC 4240382 p.Gly174Arg missense_variant 0.77
embC 4240612 c.750C>T synonymous_variant 0.4
embC 4240671 p.Thr270Ile missense_variant 0.38
embC 4241843 p.Leu661Ile missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 0.25
embA 4244379 p.Pro383Ser missense_variant 0.22
embB 4246864 c.351C>T synonymous_variant 0.32
embB 4247646 p.Glu378Ala missense_variant 0.2
aftB 4269351 c.-515C>T upstream_gene_variant 0.26
ubiA 4269387 p.Glu149Asp missense_variant 0.28
aftB 4269522 c.-686C>T upstream_gene_variant 0.3
aftB 4269606 c.-770T>C upstream_gene_variant 0.28
ethA 4326465 p.Ile337Val missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338602 c.-81A>C upstream_gene_variant 0.18
gid 4407588 c.615A>G synonymous_variant 0.24
gid 4407775 p.Asp143Gly missense_variant 0.26
gid 4408034 p.Glu57Lys missense_variant 0.22
gid 4408156 p.Leu16Arg missense_variant 0.82