TB-Profiler result

Run: ERR11466070
Summary

Run ID: ERR11466070

Sample name:

Date: 03-01-2024 13:40:09

Number of reads: 4311309

Percentage reads mapped: 99.3

Strain: lineage4.3.4.1

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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.99
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 8250 p.Glu317Gln missense_variant 0.92
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9377 c.2076A>G synonymous_variant 0.12
rpoB 761561 c.1755C>G synonymous_variant 0.14
rpoB 761564 c.1758G>C synonymous_variant 0.14
rpoB 761573 c.1767C>G synonymous_variant 0.13
rpoB 761579 c.1773G>T synonymous_variant 0.13
rpoB 761645 c.1839C>G synonymous_variant 0.12
rpoB 761948 c.2142G>C synonymous_variant 0.12
rpoB 761954 c.2148C>G synonymous_variant 0.12
rpoC 763169 c.-201A>G upstream_gene_variant 0.12
rpoC 764539 c.1170C>G synonymous_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 0.93
rpoC 765611 p.His748Tyr missense_variant 0.12
rpoC 765904 c.2535C>G synonymous_variant 0.12
rpoC 765937 c.2568T>C synonymous_variant 0.12
rpoC 766363 c.2994G>T synonymous_variant 0.13
rpoC 766381 c.3012C>T synonymous_variant 0.13
rpoC 766384 c.3015A>G synonymous_variant 0.13
rpoC 766390 c.3021C>T synonymous_variant 0.15
rpoC 766408 c.3039C>T synonymous_variant 0.19
rpoC 766426 c.3057C>T synonymous_variant 0.18
rpoC 766435 p.Glu1022Asp missense_variant 0.2
rpoC 766456 c.3087C>G synonymous_variant 0.17
rpoC 766459 c.3090G>T synonymous_variant 0.14
rpoC 766484 p.Val1039Ile missense_variant 0.18
rpoC 766843 c.3474T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.15
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.17
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.17
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.14
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.14
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.4
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.43
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.45
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.45
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.22
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.19
rrl 1474708 n.1052dupG non_coding_transcript_exon_variant 0.2
rrl 1474711 n.1054_1055insA non_coding_transcript_exon_variant 0.19
rrl 1474715 n.1061delA non_coding_transcript_exon_variant 0.19
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.41
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.39
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.42
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.45
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.43
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.43
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.19
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.13
rrl 1475209 n.1552G>A non_coding_transcript_exon_variant 0.15
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.15
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.16
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.25
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.12
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.19
rpsA 1834489 c.948T>C synonymous_variant 0.13
rpsA 1834498 c.957C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.14
kasA 2518609 p.Met165Ile missense_variant 0.15
kasA 2518651 c.537C>G synonymous_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3877596 c.912G>C synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038997 c.1708T>C synonymous_variant 0.12
clpC1 4039003 p.Asn568Asp missense_variant 0.12
clpC1 4039022 c.1683A>G synonymous_variant 0.13
clpC1 4039085 c.1620A>G synonymous_variant 0.13
clpC1 4039090 c.1615C>T synonymous_variant 0.14
clpC1 4039142 c.1563A>G synonymous_variant 0.13
clpC1 4039145 c.1560G>T synonymous_variant 0.12
clpC1 4039169 p.Glu512Asp missense_variant 0.14
clpC1 4039183 c.1522T>C synonymous_variant 0.14
clpC1 4039187 c.1518G>C synonymous_variant 0.14
clpC1 4039243 c.1462C>T synonymous_variant 0.17
clpC1 4039991 c.714G>A synonymous_variant 0.99
clpC1 4040057 c.648C>T synonymous_variant 0.14
clpC1 4040423 c.282A>G synonymous_variant 0.13
clpC1 4040431 c.274T>C synonymous_variant 0.15
clpC1 4040441 c.264C>T synonymous_variant 0.17
clpC1 4040444 c.261C>G synonymous_variant 0.17
clpC1 4040450 c.255A>G synonymous_variant 0.19
clpC1 4040456 c.249C>T synonymous_variant 0.18
clpC1 4040459 c.246C>A synonymous_variant 0.19
clpC1 4040465 c.240T>C synonymous_variant 0.18
clpC1 4040471 c.234T>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247463 p.Ser317Cys missense_variant 0.11
embB 4247470 c.957T>C synonymous_variant 0.15
embB 4247491 c.978G>C synonymous_variant 0.12
embB 4247497 c.984T>C synonymous_variant 0.12
embB 4247500 c.987C>G synonymous_variant 0.12
embB 4248264 p.Phe584Ser missense_variant 0.13
embB 4248275 p.Thr588Ala missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0