TB-Profiler result

Run: ERR1950088
Summary

Run ID: ERR1950088

Sample name:

Date: 31-03-2023 15:39:32

Number of reads: 335896

Percentage reads mapped: 99.68

Strain: lineage4

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
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 7448 p.Lys49Asn missense_variant 0.4
mshA 575266 c.-81_-79delGCT upstream_gene_variant 0.17
mshA 575308 c.-40A>T upstream_gene_variant 0.22
mshA 575714 p.Tyr123Asn missense_variant 0.2
ccsA 620525 c.637delG frameshift_variant 0.22
rpoB 760651 p.Thr282Ile missense_variant 0.12
rpoB 761771 p.Met655Ile missense_variant 0.33
rpoC 763700 p.Pro111Ser missense_variant 0.14
rpoC 764053 p.Lys228Asn missense_variant 0.25
rpoC 765238 c.1869C>T synonymous_variant 0.17
rpoC 765339 p.Gln657Arg missense_variant 0.2
rpoC 765889 c.2520C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776259 p.Ala741Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304819 p.Val630Ala missense_variant 0.14
Rv1258c 1406212 p.His377Asn missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471735 n.-111T>A upstream_gene_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474726 n.1069A>G non_coding_transcript_exon_variant 0.12
rrl 1475199 n.1543delT non_coding_transcript_exon_variant 0.13
rrl 1475999 n.2342G>A non_coding_transcript_exon_variant 0.29
rpsA 1833724 c.183C>T synonymous_variant 0.17
rpsA 1834155 p.Asn205Ser missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918565 p.Leu209Pro missense_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169125 c.1488T>A synonymous_variant 0.4
PPE35 2169360 p.Asn418Ile missense_variant 0.15
PPE35 2169797 c.816G>T synonymous_variant 0.29
Rv1979c 2223110 p.Val19Ile missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714379 c.954C>T synonymous_variant 0.15
folC 2747264 p.Gly112Asp missense_variant 0.4
folC 2747601 c.-3G>A upstream_gene_variant 0.29
pepQ 2860592 c.-174T>A upstream_gene_variant 0.4
fprA 3474274 p.Pro90Ser missense_variant 0.12
fprA 3474936 c.930C>T synonymous_variant 0.2
fbiB 3641953 p.Leu140Arg missense_variant 0.29
alr 3840578 c.843T>A synonymous_variant 0.15
ddn 3987160 p.Val106Ala missense_variant 0.12
clpC1 4040510 p.Glu65Asp missense_variant 0.12
clpC1 4040876 c.-172T>C upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245349 p.Ala706Gly missense_variant 0.11
embB 4247028 p.Leu172Pro missense_variant 0.5
aftB 4267120 p.Ala573Thr missense_variant 0.33
aftB 4268143 p.Tyr232His missense_variant 0.2
ethR 4327685 p.Ser46Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0