TB-Profiler result

Run: ERR4818936
Summary

Run ID: ERR4818936

Sample name:

Date: 01-04-2023 15:50:05

Number of reads: 587752

Percentage reads mapped: 96.17

Strain: lineage4.1.2.1

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 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.96
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.5 streptomycin
ethA 4326005 c.1468delT frameshift_variant&stop_lost&splice_region_variant 0.13 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8890 p.Lys530Arg missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490607 c.-176G>A upstream_gene_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619835 c.-56G>T upstream_gene_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760865 c.1059C>T synonymous_variant 0.17
rpoB 760909 p.Gly368Val missense_variant 0.11
rpoB 762879 p.Met1025Leu missense_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781516 c.-44C>T upstream_gene_variant 0.12
fbiC 1305445 p.Gly839Ser missense_variant 0.12
Rv1258c 1406815 p.Ile176Val missense_variant 0.12
Rv1258c 1407031 c.310C>T synonymous_variant 0.17
atpE 1461162 p.Ala40Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.33
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.29
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.4
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.4
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.71
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.71
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.71
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.71
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.6
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.75
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.57
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.86
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.57
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.29
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.8
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.67
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.5
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.33
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.67
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.79
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.8
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.8
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.8
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.6
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.8
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.75
rrl 1473534 n.-124T>C upstream_gene_variant 0.29
rrl 1474261 n.604C>A non_coding_transcript_exon_variant 0.67
rrl 1475132 n.1475T>C non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25
rpsA 1834268 p.Lys243Glu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918490 p.Gln184Arg missense_variant 0.11
PPE35 2168115 p.Gly833Asp missense_variant 0.11
PPE35 2169337 p.Asp426His missense_variant 0.11
PPE35 2170544 c.69G>A synonymous_variant 0.11
Rv1979c 2222841 c.324G>T synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290099 c.-858C>T upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.17
folC 2746845 p.Ala252Thr missense_variant 0.13
ribD 2987015 c.177C>T synonymous_variant 0.12
ribD 2987468 c.630G>A synonymous_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087151 p.Gly111Asp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568567 p.Val38Ala missense_variant 0.12
Rv3236c 3612950 p.Glu56Val missense_variant 0.13
fbiA 3641104 p.Val188Phe missense_variant 1.0
alr 3840279 p.Asp381Gly missense_variant 0.12
clpC1 4039161 p.His515Gly missense_variant 0.11
clpC1 4039169 p.Glu512Asp missense_variant 0.11
clpC1 4039691 c.1014G>C synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242721 c.-512G>C upstream_gene_variant 0.14
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245202 p.Thr657Ile missense_variant 0.12
embA 4246296 p.Gln1022* stop_gained 0.18
embB 4247068 c.555T>C synonymous_variant 0.17
embB 4247090 p.Thr193Ala missense_variant 0.14
embB 4247512 c.999T>C synonymous_variant 0.12
embB 4247516 p.Asn335Asp missense_variant 0.12
aftB 4268495 c.342G>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0