TB-Profiler result

Run: ERR2179707
Summary

Run ID: ERR2179707

Sample name:

Date: 15-08-2022 11:55:54

Number of reads: 426797

Percentage reads mapped: 23.14

Strain: lineage4.4.2

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 1.0
lineage4.4 Euro-American S;T None 0.99
lineage4.4.2 Euro-American T1;T2 None 1.0
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
ethA 4327411 p.Trp21* stop_gained 0.17 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
gyrA 8783 c.1482G>T synonymous_variant 0.17
gyrA 9691 p.Gln797Arg missense_variant 0.17
fgd1 490967 p.Gly62Asp missense_variant 0.18
ccsA 620150 p.Gly87Val missense_variant 0.17
rpoB 760339 p.Gly178Val missense_variant 0.2
rpoC 763575 p.Arg69Leu missense_variant 0.18
rpoC 764803 c.1434C>T synonymous_variant 0.12
rpoC 765482 p.Pro705Thr missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800727 c.-82C>T upstream_gene_variant 0.17
rplC 801013 p.Gln69* stop_gained 0.2
fbiC 1302852 c.-79C>A upstream_gene_variant 0.12
fbiC 1302870 c.-61G>T upstream_gene_variant 0.12
fbiC 1303043 p.Thr38Lys missense_variant 0.2
fbiC 1303215 c.285C>A synonymous_variant 0.12
embR 1416971 p.Ala126Val missense_variant 0.12
atpE 1460848 c.-197C>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472944 n.1099G>A non_coding_transcript_exon_variant 0.17
rrs 1472984 n.1139C>T non_coding_transcript_exon_variant 0.12
ndh 2102032 c.1011C>A synonymous_variant 0.2
ndh 2102037 p.Ala336Thr missense_variant 0.2
ndh 2102041 p.Gln334His missense_variant 0.18
katG 2154718 p.Ser465Leu missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223346 c.-182C>T upstream_gene_variant 0.2
kasA 2517947 c.-168C>A upstream_gene_variant 0.12
eis 2715573 c.-241G>T upstream_gene_variant 0.18
ahpC 2726115 c.-78C>A upstream_gene_variant 0.13
pepQ 2860423 c.-5G>T upstream_gene_variant 0.2
ribD 2986989 p.Gly51Cys missense_variant 0.2
Rv2752c 3065033 p.Gly387Trp missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448485 c.-19C>A upstream_gene_variant 0.25
fprA 3475072 p.Val356Ile missense_variant 0.18
whiB7 3568593 p.Phe29Leu missense_variant 0.17
whiB7 3568792 c.-113C>A upstream_gene_variant 0.13
Rv3236c 3612687 p.Gly144Ser missense_variant 0.2
fbiB 3642418 p.Thr295Ile missense_variant 0.2
alr 3840283 p.Ala380Ser missense_variant 0.13
ddn 3986944 p.Gly34Val missense_variant 0.2
panD 4043997 c.285C>T synonymous_variant 0.12
embB 4246735 c.222G>T synonymous_variant 0.18
embB 4247370 p.Gly286Val missense_variant 0.18
embB 4248564 p.Ala684Asp missense_variant 0.12
embB 4248594 p.Gly694Val missense_variant 0.14
aftB 4268779 p.Gly20Trp missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0