TB-Profiler result

Run: ERR4811990
Summary

Run ID: ERR4811990

Sample name:

Date: 01-04-2023 11:47:37

Number of reads: 759682

Percentage reads mapped: 99.4

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8223 p.Asp308His missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.38
ccsA 619837 c.-54G>T upstream_gene_variant 0.13
ccsA 620114 p.Arg75Pro missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760555 p.Glu250Gly missense_variant 1.0
rpoB 761724 c.1921delA frameshift_variant 0.17
rpoC 762476 c.-894C>A upstream_gene_variant 0.13
rpoC 762521 c.-849C>A upstream_gene_variant 0.13
rpoC 763172 c.-198G>T upstream_gene_variant 0.13
rpoC 764457 p.Pro363Gln missense_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765490 c.2121C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776582 p.Gln633His missense_variant 0.12
mmpL5 776867 c.1614G>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781809 p.Gly84Arg missense_variant 0.12
rplC 801166 p.Gly120Cys missense_variant 0.15
fbiC 1302920 c.-11G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473694 n.37C>T non_coding_transcript_exon_variant 0.17
rrl 1473868 n.211C>T non_coding_transcript_exon_variant 1.0
rpsA 1834129 c.588C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154437 p.Ala559Thr missense_variant 0.11
katG 2154551 p.Leu521Met missense_variant 0.18
katG 2156532 c.-421C>T upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289873 c.-632C>A upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746277 p.Asp441Gly missense_variant 1.0
folC 2746849 c.750G>C synonymous_variant 0.11
pepQ 2860406 p.Gln5Lys missense_variant 0.17
Rv2752c 3065999 p.Arg65Cys missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087862 p.Gly348Val missense_variant 0.15
fbiD 3339402 c.285C>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474104 p.Asp33Gly missense_variant 0.13
fbiA 3640849 p.Glu103* stop_gained 0.12
fbiB 3641358 c.-177G>T upstream_gene_variant 0.14
alr 3840661 p.Gly254Cys missense_variant 0.12
rpoA 3878163 c.345C>A synonymous_variant 0.14
rpoA 3878413 p.Tyr32Cys missense_variant 0.13
clpC1 4039737 p.Thr323Asn missense_variant 0.11
embC 4241537 p.Gly559Arg missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243896 p.Ala222Ser missense_variant 0.11
embB 4246928 p.Gln139Lys missense_variant 0.11
embB 4247028 p.Leu172Arg missense_variant 0.23
embB 4247055 p.Leu181Gln missense_variant 0.2
embB 4249766 p.Arg1085Ser missense_variant 0.12
aftB 4269282 c.-446G>T upstream_gene_variant 0.12
ubiA 4269380 p.Val152Ile missense_variant 0.13
ethA 4328308 c.-835G>T upstream_gene_variant 0.12
ethA 4328416 c.-943G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408283 c.-81A>G upstream_gene_variant 1.0
gid 4408388 c.-186C>T upstream_gene_variant 0.12