TB-Profiler result

Run: ERR4820565
Summary

Run ID: ERR4820565

Sample name:

Date: 01-04-2023 16:45:07

Number of reads: 266473

Percentage reads mapped: 98.65

Strain: lineage4.1.2.1

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 1.0
lineage4.1.2 Euro-American T;H None 1.0
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
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 5159 c.-81C>T upstream_gene_variant 0.2
gyrB 7050 p.Glu604Gly missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490697 c.-86C>T upstream_gene_variant 0.5
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619830 c.-61_-60delGTinsTG upstream_gene_variant 0.29
ccsA 620605 c.719delT frameshift_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775737 p.Leu915Pro missense_variant 0.29
mmpL5 776634 p.Asp616Gly missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303330 c.400C>A synonymous_variant 0.15
fbiC 1304727 c.1797A>G synonymous_variant 0.33
fbiC 1304742 c.1812T>C synonymous_variant 0.33
atpE 1461078 p.Gly12Arg missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833738 p.Arg66His missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918359 c.420A>T synonymous_variant 0.25
PPE35 2169240 p.Pro458Leu missense_variant 1.0
PPE35 2170778 c.-166A>G upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715186 c.147C>A synonymous_variant 0.2
ahpC 2725967 c.-226G>A upstream_gene_variant 0.15
ahpC 2725992 c.-201G>A upstream_gene_variant 0.13
Rv2752c 3065905 p.Leu96Pro missense_variant 0.18
Rv2752c 3066000 p.Met64Ile missense_variant 0.25
thyA 3074645 c.-174T>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038838 c.1867C>T synonymous_variant 1.0
clpC1 4038845 c.1858_1860delTCGinsAGC synonymous_variant 1.0
clpC1 4038857 c.1848C>G synonymous_variant 0.67
clpC1 4038860 c.1845G>C synonymous_variant 0.67
embC 4240644 p.Arg261Pro missense_variant 0.25
embC 4241476 c.1614G>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408421 c.-219C>A upstream_gene_variant 1.0