TB-Profiler result

Run: ERR4407467

Summary

Run ID: ERR4407467

Sample name:

Date: 01-04-2023 05:45:19

Number of reads: 254971

Percentage reads mapped: 99.45

Strain: lineage4.3.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.1 Euro-American (LAM) LAM9 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
gyrB 6932 p.Gln565Lys missense_variant 0.29
gyrA 7303 c.2T>C start_lost 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8879 c.1580delA frameshift_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491092 p.Gly104Ser missense_variant 0.12
fgd1 491665 p.Glu295* stop_gained 0.14
mshA 576672 p.Arg442Gln missense_variant 0.18
rpoC 764192 p.Glu275Lys missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 0.95
rpoC 767123 p.Val1252Met missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775861 p.Met874Val missense_variant 0.13
mmpL5 778458 p.Ala8Val missense_variant 0.12
mmpR5 779036 p.Ile16Thr missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781531 c.-29T>C upstream_gene_variant 0.12
fbiC 1304829 c.1899T>C synonymous_variant 0.15
fbiC 1305335 p.Gly802Asp missense_variant 0.18
Rv1258c 1407376 c.-36C>T upstream_gene_variant 1.0
embR 1416644 p.Leu235Pro missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472999 n.1154C>A non_coding_transcript_exon_variant 0.12
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.4
rrl 1476477 n.2820G>A non_coding_transcript_exon_variant 0.2
rpsA 1834758 p.Gly406Ala missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101766 p.Arg426His missense_variant 0.12
PPE35 2170066 p.Ala183Thr missense_variant 0.27
PPE35 2170565 c.47delT frameshift_variant 0.18
Rv1979c 2222825 c.339delC frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747438 p.Met54Thr missense_variant 1.0
Rv2752c 3065237 p.Ser319Pro missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074533 c.-62G>A upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087625 p.Ile269Thr missense_variant 0.12
fbiD 3339559 p.Thr148Ala missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641340 c.-195T>C upstream_gene_variant 0.1
fbiB 3642441 p.Pro303Thr missense_variant 0.15
alr 3840869 c.552C>T synonymous_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040719 c.-16delG upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245993 p.Ala921Ser missense_variant 0.14
embB 4248449 c.1938dupG frameshift_variant 0.11
ethR 4327336 c.-213A>G upstream_gene_variant 0.11
ethA 4328364 c.-891C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407857 p.Arg116Trp missense_variant 1.0
gid 4407917 p.Arg96Ser missense_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 1.0