TB-Profiler result

Run: ERR9786771
Summary

Run ID: ERR9786771

Sample name:

Date: 02-04-2023 12:44:09

Number of reads: 2342937

Percentage reads mapped: 99.66

Strain: lineage6.1.1;lineage4.3.4.1

Drug-resistance: Sensitive

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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 0.73
lineage6 West-Africa 2 AFRI_1 RD702 0.31
lineage4.3 Euro-American (LAM) mainly-LAM None 0.71
lineage6.1.1 West-Africa 2 AFRI_1 RD702 0.33
lineage4.3.4 Euro-American (LAM) LAM RD174 0.7
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.7
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
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 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8493 p.Leu398Phe missense_variant 0.28
gyrA 8715 p.Pro472Ser missense_variant 0.71
gyrA 9143 c.1842T>C synonymous_variant 0.26
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491668 p.Lys296Glu missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 0.31
rpoB 759608 c.-199C>T upstream_gene_variant 0.78
rpoB 760855 p.Thr350Ile missense_variant 0.26
rpoB 760969 p.Ser388Leu missense_variant 0.22
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoB 761723 p.Glu639Asp missense_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 0.73
rpoC 766231 c.2862T>C synonymous_variant 0.32
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
fbiC 1302899 c.-32A>G upstream_gene_variant 0.31
Rv1258c 1406685 p.Val219Ala missense_variant 0.27
embR 1416633 p.Leu239Val missense_variant 0.22
atpE 1461251 c.207G>T synonymous_variant 0.34
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674434 p.Val78Ala missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.29
katG 2155503 c.609C>T synonymous_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 0.26
Rv1979c 2222308 p.Asp286Gly missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289706 c.-465C>A upstream_gene_variant 0.36
kasA 2518132 c.18C>T synonymous_variant 0.19
ahpC 2726323 p.Pro44Arg missense_variant 0.73
pepQ 2859830 p.Gly197Arg missense_variant 0.65
thyA 3073868 p.Thr202Ala missense_variant 0.73
ald 3086728 c.-92C>T upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.23
ald 3087518 c.699C>T synonymous_variant 0.59
Rv3083 3448598 p.Ile32Thr missense_variant 0.65
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.3
Rv3236c 3612009 p.Ala370Thr missense_variant 0.68
Rv3236c 3612143 p.Arg325His missense_variant 0.23
Rv3236c 3612768 p.Ala117Pro missense_variant 0.68
alr 3840264 p.Ile386Thr missense_variant 0.3
alr 3841006 p.Asp139His missense_variant 0.72
clpC1 4038287 c.2418C>T synonymous_variant 0.74
embC 4240671 p.Thr270Ile missense_variant 0.34
embC 4241843 p.Leu661Ile missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243570 p.Thr113Arg missense_variant 0.27
embA 4244220 c.988C>T synonymous_variant 0.27
embA 4244379 p.Pro383Ser missense_variant 0.25
embB 4246864 c.351C>T synonymous_variant 0.34
embB 4247646 p.Glu378Ala missense_variant 0.32
aftB 4269351 c.-515C>T upstream_gene_variant 0.3
ubiA 4269387 p.Glu149Asp missense_variant 0.31
aftB 4269522 c.-686C>T upstream_gene_variant 0.34
aftB 4269606 c.-770T>C upstream_gene_variant 0.3
ethA 4326465 p.Ile337Val missense_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.28
gid 4408034 p.Glu57Lys missense_variant 0.27
gid 4408156 p.Leu16Arg missense_variant 0.67