TB-Profiler result

Run: ERR2514060
Summary

Run ID: ERR2514060

Sample name:

Date: 31-03-2023 20:05:37

Number of reads: 679166

Percentage reads mapped: 99.56

Strain: lineage4.1.1.3.1

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 1.0
lineage4.1 Euro-American T;X;H None 0.96
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.98
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.97
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 0.97
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 7464 p.Val55Leu missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9309 p.Asp670Asn missense_variant 0.18
gyrA 9675 p.Arg792Cys missense_variant 0.11
fgd1 490751 c.-32T>G upstream_gene_variant 0.18
mshA 576551 p.Ile402Val missense_variant 0.15
mshA 576751 p.Lys468Asn missense_variant 0.22
ccsA 620719 p.Ala277Ser missense_variant 0.22
rpoB 762179 c.2373C>T synonymous_variant 0.15
rpoB 762251 c.2445G>T synonymous_variant 0.13
rpoB 763081 p.Gly1092Val missense_variant 0.12
rpoC 764540 p.Val391Ile missense_variant 0.22
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765815 p.Thr816Ala missense_variant 0.1
rpoC 767287 c.3918G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777864 p.Val206Glu missense_variant 0.13
mmpR5 778088 c.-902C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303182 c.252C>A synonymous_variant 0.12
fbiC 1303601 p.Glu224Gly missense_variant 1.0
fbiC 1305020 p.Ala697Asp missense_variant 0.12
Rv1258c 1406154 c.1186delC frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833869 p.Glu110* stop_gained 0.11
tlyA 1917822 c.-118G>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102002 c.1041C>T synonymous_variant 0.17
katG 2156355 c.-244C>A upstream_gene_variant 0.25
katG 2156401 c.-290C>T upstream_gene_variant 0.12
PPE35 2169044 c.1569G>C synonymous_variant 0.12
PPE35 2170066 p.Ala183Thr missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288728 p.Leu172Met missense_variant 0.11
pncA 2289062 c.180C>T synonymous_variant 0.12
pncA 2289985 c.-744G>A upstream_gene_variant 0.2
eis 2714903 p.Arg144Gly missense_variant 0.14
ahpC 2726506 p.Thr105Lys missense_variant 0.11
ahpC 2726567 c.375C>A synonymous_variant 0.14
folC 2746750 c.849C>T synonymous_variant 0.2
pepQ 2859715 p.Arg235His missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087112 p.Ala98Val missense_variant 0.11
fbiD 3339120 c.3G>T start_lost 0.15
Rv3083 3448606 p.Leu35Met missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475262 p.Thr419Lys missense_variant 0.12
whiB7 3568623 c.57G>A synonymous_variant 0.11
Rv3236c 3611993 p.Gly375Val missense_variant 0.13
Rv3236c 3612929 p.Pro63His missense_variant 0.12
fbiB 3642243 p.Ala237Thr missense_variant 0.12
fbiB 3642596 c.1062C>T synonymous_variant 0.18
fbiB 3642707 c.1176delG frameshift_variant 0.13
alr 3841058 c.363G>T synonymous_variant 0.18
rpoA 3878285 p.Glu75Lys missense_variant 0.12
ddn 3986681 c.-163C>T upstream_gene_variant 0.14
ddn 3987074 c.231C>T synonymous_variant 0.16
clpC1 4038177 p.Pro843Leu missense_variant 0.29
clpC1 4038266 c.2439C>A synonymous_variant 0.15
embC 4239865 c.3G>A start_lost 0.11
embC 4241689 c.1827G>T synonymous_variant 0.11
embC 4242230 p.Ile790Phe missense_variant 0.15
embC 4242566 p.Thr902Ala missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.89
embB 4246834 p.Lys107Asn missense_variant 0.13
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249742 p.Gln1077Lys missense_variant 0.13
aftB 4267045 p.Thr598Ala missense_variant 0.11
aftB 4267561 p.Ala426Thr missense_variant 0.12
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
ethR 4327898 p.His117Arg missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0