TB-Profiler result

Run: ERR9787220
Summary

Run ID: ERR9787220

Sample name:

Date: 02-04-2023 13:05:19

Number of reads: 679108

Percentage reads mapped: 99.49

Strain: lineage6;lineage4.1

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 0.37
lineage6 West-Africa 2 AFRI_1 RD702 0.7
lineage4.1 Euro-American T;X;H None 0.24
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 0.67 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 6002 p.Gly255Ser missense_variant 0.31
gyrB 6446 p.Ala403Ser missense_variant 0.72
gyrB 6507 p.Ala423Val missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8402 c.1101C>T synonymous_variant 0.69
gyrA 8493 p.Leu398Phe missense_variant 0.71
gyrA 9143 c.1842T>C synonymous_variant 0.7
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9656 c.2355C>G synonymous_variant 0.3
fgd1 491668 p.Lys296Glu missense_variant 0.69
fgd1 491742 c.960T>C synonymous_variant 0.57
mshA 575884 c.537G>C synonymous_variant 0.11
ccsA 620213 p.Gly108Val missense_variant 0.11
rpoB 760855 p.Thr350Ile missense_variant 0.59
rpoB 760969 p.Ser388Leu missense_variant 0.65
rpoB 761723 p.Glu639Asp missense_variant 0.59
rpoC 762569 c.-801C>T upstream_gene_variant 0.38
rpoC 763031 c.-339T>C upstream_gene_variant 0.71
rpoC 765150 p.Gly594Glu missense_variant 0.38
rpoC 765187 c.1818C>T synonymous_variant 0.32
rpoC 766012 c.2643C>G synonymous_variant 0.11
rpoC 766231 c.2862T>C synonymous_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpR5 779453 c.464_465insC frameshift_variant 0.7
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.24
fbiC 1302899 c.-32A>G upstream_gene_variant 0.66
Rv1258c 1406685 p.Val219Ala missense_variant 0.82
embR 1416633 p.Leu239Val missense_variant 0.68
atpE 1461251 c.207G>T synonymous_variant 0.8
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473905 n.248T>A non_coding_transcript_exon_variant 0.13
rrl 1475495 n.1838A>G non_coding_transcript_exon_variant 0.12
inhA 1674434 p.Val78Ala missense_variant 0.92
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.68
katG 2155503 c.609C>T synonymous_variant 0.61
katG 2156007 c.105C>T synonymous_variant 0.24
PPE35 2167926 p.Leu896Ser missense_variant 0.62
Rv1979c 2222308 p.Asp286Gly missense_variant 0.74
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.56
ald 3086728 c.-92C>T upstream_gene_variant 0.72
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.58
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.74
whiB7 3568791 c.-112G>A upstream_gene_variant 0.11
Rv3236c 3612143 p.Arg325His missense_variant 0.74
embC 4240671 p.Thr270Ile missense_variant 0.65
embC 4241843 p.Leu661Ile missense_variant 0.83
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.32
embA 4244220 c.988C>T synonymous_variant 0.84
embA 4244379 p.Pro383Ser missense_variant 0.74
embB 4246864 c.351C>T synonymous_variant 0.59
embB 4247646 p.Glu378Ala missense_variant 0.78
aftB 4269351 c.-515C>T upstream_gene_variant 0.82
ubiA 4269387 p.Glu149Asp missense_variant 0.82
aftB 4269522 c.-686C>T upstream_gene_variant 0.78
aftB 4269606 c.-770T>C upstream_gene_variant 0.78
ethA 4326465 p.Ile337Val missense_variant 0.76
ethA 4328091 c.-618C>T upstream_gene_variant 0.3
whiB6 4338193 p.Arg110Leu missense_variant 0.79
whiB6 4338391 p.Thr44Ile missense_variant 0.47
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.57
gid 4408034 p.Glu57Lys missense_variant 0.96