TB-Profiler result

Run: ERR2229726
Summary

Run ID: ERR2229726

Sample name:

Date: 31-03-2023 17:29:22

Number of reads: 541957

Percentage reads mapped: 99.19

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8161 p.Ile287Asn missense_variant 0.25
fgd1 491745 c.963G>A synonymous_variant 0.33
rpoB 762037 p.Ile744Thr missense_variant 0.29
rpoC 763445 p.Gly26Cys missense_variant 0.12
rpoC 765015 p.Ala549Val missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775990 p.Leu831Met missense_variant 0.22
mmpL5 776149 p.Ile778Phe missense_variant 0.29
mmpL5 776616 p.Pro622Leu missense_variant 0.15
mmpS5 779530 c.-625C>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781729 p.Leu57* stop_gained 0.17
rpsL 781812 p.Gly85Ser missense_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305388 p.Ala820Ser missense_variant 0.2
Rv1258c 1407408 c.-68G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472461 n.616G>T non_coding_transcript_exon_variant 0.13
rrl 1473429 n.-229G>A upstream_gene_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474570 n.913G>C non_coding_transcript_exon_variant 0.18
rrl 1475183 n.1526A>T non_coding_transcript_exon_variant 0.13
rrl 1475898 n.2241A>T non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.41
inhA 1674042 c.-160G>T upstream_gene_variant 0.5
fabG1 1674183 c.744A>G stop_lost&splice_region_variant 0.14
rpsA 1834084 p.Asn181Lys missense_variant 0.13
rpsA 1834724 p.Gly395Cys missense_variant 0.17
tlyA 1917905 c.-35C>A upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918097 p.Thr53Asn missense_variant 0.18
ndh 2102038 c.1005C>A synonymous_variant 0.25
katG 2156021 p.Glu31Lys missense_variant 0.12
katG 2156136 c.-25A>G upstream_gene_variant 0.14
PPE35 2167955 c.2658A>C synonymous_variant 0.22
PPE35 2167973 c.2640A>G synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.3
PPE35 2169272 c.1341C>G synonymous_variant 0.3
PPE35 2169278 c.1335T>C synonymous_variant 0.33
PPE35 2169281 c.1332T>G synonymous_variant 0.3
PPE35 2169304 p.Met437Leu missense_variant 0.15
PPE35 2169890 c.723C>T synonymous_variant 0.12
PPE35 2169893 c.720C>A synonymous_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.9
PPE35 2170053 p.Thr187Ser missense_variant 0.9
PPE35 2170189 p.Glu142Gln missense_variant 0.22
PPE35 2170190 c.423G>A synonymous_variant 0.22
PPE35 2170528 p.Ser29Ala missense_variant 0.12
Rv1979c 2221747 p.Arg473Leu missense_variant 0.17
Rv1979c 2222298 c.867G>T synonymous_variant 0.4
Rv1979c 2222647 p.Ala173Glu missense_variant 0.22
Rv1979c 2222749 p.Leu139Pro missense_variant 0.29
Rv1979c 2222782 p.Ala128Val missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289137 c.105G>A synonymous_variant 0.25
pncA 2289966 c.-725G>T upstream_gene_variant 0.25
ahpC 2726168 c.-25G>A upstream_gene_variant 0.15
ahpC 2726658 p.Arg156Ser missense_variant 0.15
ribD 2987339 c.501C>T synonymous_variant 0.33
Rv2752c 3064688 p.Lys502Glu missense_variant 0.17
thyX 3067858 p.Asp30Tyr missense_variant 0.29
thyX 3068033 c.-88T>G upstream_gene_variant 0.17
fbiD 3338929 c.-189A>G upstream_gene_variant 0.14
Rv3236c 3612722 p.Val132Glu missense_variant 0.22
fbiB 3640617 c.-918G>T upstream_gene_variant 0.33
fbiB 3641597 c.63C>T synonymous_variant 0.15
alr 3840435 p.Leu329Arg missense_variant 0.25
clpC1 4038487 p.Gly740Ser missense_variant 0.29
clpC1 4039691 c.1014G>C synonymous_variant 0.25
clpC1 4039876 p.Asn277Asp missense_variant 0.12
clpC1 4040057 c.648C>T synonymous_variant 0.33
clpC1 4040867 c.-163A>G upstream_gene_variant 0.17
embC 4239963 c.103delG frameshift_variant 0.14
embC 4240509 p.Ala216Val missense_variant 0.12
embC 4241666 p.Ala602Ser missense_variant 0.33
embC 4241738 p.Val626Leu missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245223 p.Tyr664Cys missense_variant 0.17
embB 4246567 c.54_55insT frameshift_variant 0.33
embB 4247512 c.999T>C synonymous_variant 0.2
embB 4247516 p.Asn335Asp missense_variant 0.22
embB 4248116 p.Gly535Cys missense_variant 0.18
embB 4248152 p.Ala547Thr missense_variant 0.13
aftB 4268198 c.639C>T synonymous_variant 0.15
ubiA 4270011 c.-178A>G upstream_gene_variant 0.22
ubiA 4270016 c.-183G>A upstream_gene_variant 0.22
ubiA 4270021 c.-188T>C upstream_gene_variant 0.2
ubiA 4270026 c.-193C>T upstream_gene_variant 0.2
ethA 4326333 p.Ala381Ser missense_variant 0.18
ethA 4326474 p.Pro334Thr missense_variant 0.15
ethA 4327193 p.Ile94Asn missense_variant 0.4
ethA 4327227 p.Glu83Lys missense_variant 0.33
ethA 4327920 c.-447A>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0