TB-Profiler result

Run: ERR2229149
Summary

Run ID: ERR2229149

Sample name:

Date: 31-03-2023 16:44:38

Number of reads: 432387

Percentage reads mapped: 99.43

Strain: lineage4.8

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 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 5814 p.Arg192His missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7378 p.Arg26His missense_variant 0.14
gyrA 7694 c.393A>G synonymous_variant 0.25
gyrA 8709 p.Ala470Ser missense_variant 0.18
gyrA 9462 p.Thr721Ser missense_variant 0.2
ccsA 620124 c.234G>T synonymous_variant 0.4
ccsA 620663 p.Tyr258Cys missense_variant 0.14
rpoB 759636 c.-171C>T upstream_gene_variant 0.14
rpoB 760086 p.Ser94Pro missense_variant 0.11
rpoB 761502 p.Pro566Thr missense_variant 0.33
rpoB 761603 c.1797C>A synonymous_variant 0.29
rpoC 763106 c.-264C>T upstream_gene_variant 0.17
rpoC 764158 p.Lys263Asn missense_variant 0.17
rpoC 765021 p.Ala551Glu missense_variant 0.13
rpoC 765502 p.Gln711His missense_variant 0.29
rpoC 766282 p.Ser971Arg missense_variant 0.22
rpoC 766531 c.3162G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777246 p.Arg412Gln missense_variant 0.4
mmpL5 777601 p.Asp294Tyr missense_variant 0.18
mmpL5 777655 p.Asp276Tyr missense_variant 0.17
mmpL5 778741 c.-261G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303722 c.792C>A synonymous_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303855 p.Ala309Thr missense_variant 0.29
fbiC 1304031 c.1101C>T synonymous_variant 0.22
Rv1258c 1406447 c.894G>T synonymous_variant 0.18
embR 1416929 p.Ala140Asp missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834174 c.633C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918067 p.Ala43Gly missense_variant 0.4
tlyA 1918519 p.Pro194Thr missense_variant 0.14
ndh 2102044 c.999G>T synonymous_variant 0.2
ndh 2102050 c.993T>G synonymous_variant 0.2
ndh 2102452 p.Leu197Phe missense_variant 0.25
katG 2156489 c.-378C>A upstream_gene_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.4
PPE35 2167967 c.2646A>C synonymous_variant 0.4
PPE35 2167973 c.2640A>G synonymous_variant 0.4
PPE35 2167997 c.2616G>C synonymous_variant 0.22
PPE35 2168427 p.Ile729Asn missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169185 p.Ser476Arg missense_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.27
PPE35 2170232 c.381T>C synonymous_variant 0.12
PPE35 2170235 c.378T>C synonymous_variant 0.12
PPE35 2170238 c.375T>G synonymous_variant 0.12
PPE35 2170306 p.Ala103Ser missense_variant 0.12
Rv1979c 2223015 c.150C>A synonymous_variant 0.29
Rv1979c 2223230 c.-66C>A upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289708 c.-467G>C upstream_gene_variant 0.18
pncA 2289711 c.-470T>C upstream_gene_variant 0.18
eis 2714248 p.Gly362Val missense_variant 0.22
folC 2746746 p.Val285Phe missense_variant 0.4
pepQ 2859748 p.Ala224Asp missense_variant 0.4
pepQ 2860456 c.-38G>A upstream_gene_variant 0.12
ribD 2986806 c.-33G>T upstream_gene_variant 0.5
ribD 2987602 p.Tyr255Cys missense_variant 0.15
Rv2752c 3064785 c.1407G>C synonymous_variant 0.25
Rv2752c 3065006 p.Val396Met missense_variant 0.22
Rv2752c 3065705 p.Gly163Arg missense_variant 0.5
thyX 3067991 c.-46G>T upstream_gene_variant 0.22
ald 3086622 c.-198C>G upstream_gene_variant 0.33
ald 3086997 p.Thr60Gly missense_variant 0.17
fbiD 3339546 c.429G>T synonymous_variant 0.5
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3475214 p.Ala403Glu missense_variant 0.17
Rv3236c 3612582 p.Leu179Ile missense_variant 0.2
Rv3236c 3612834 p.Val95Phe missense_variant 0.22
fbiA 3641499 p.Met319Ile missense_variant 0.15
fbiB 3641798 c.264C>A synonymous_variant 0.33
alr 3840768 p.Phe218Ser missense_variant 0.25
alr 3840923 c.498C>T synonymous_variant 0.25
rpoA 3877792 p.Ala239Asp missense_variant 0.25
rpoA 3877865 p.Leu215Met missense_variant 0.12
clpC1 4038883 p.Gly608Ser missense_variant 0.22
clpC1 4040294 p.Gln137His missense_variant 0.25
clpC1 4040809 c.-105G>T upstream_gene_variant 0.13
clpC1 4040824 c.-120C>A upstream_gene_variant 0.13
panD 4044189 p.Asp31Glu missense_variant 0.2
embC 4240561 c.699C>A synonymous_variant 0.13
embC 4242017 p.Glu719Lys missense_variant 0.29
embC 4242339 p.Thr826Asn missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244103 p.Ala291Thr missense_variant 0.25
embA 4244184 p.Ser318Leu missense_variant 0.29
embA 4245705 p.His825Asn missense_variant 0.33
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4247036 p.Gly175Cys missense_variant 0.33
embB 4247147 c.637delC frameshift_variant 0.4
embB 4247949 p.Val479Gly missense_variant 0.22
aftB 4267106 c.1731T>C synonymous_variant 0.18
aftB 4268514 p.Pro108His missense_variant 0.25
ubiA 4268978 p.Leu286Met missense_variant 0.33
ubiA 4269922 c.-89C>A upstream_gene_variant 0.18
whiB6 4338406 p.Asp39Gly missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408162 p.Pro14Gln missense_variant 0.22