TB-Profiler result

Run: ERR11465627
Summary

Run ID: ERR11465627

Sample name:

Date: 10-01-2024 01:35:31

Number of reads: 2207354

Percentage reads mapped: 99.53

Strain: lineage4.3.4.2.1

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
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
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762101 c.2295C>G synonymous_variant 0.11
rpoB 762218 c.2412T>C synonymous_variant 0.13
rpoB 762224 c.2418C>G synonymous_variant 0.13
rpoB 762233 c.2427G>C synonymous_variant 0.12
rpoB 762236 c.2430G>C synonymous_variant 0.12
rpoB 762251 c.2445G>C synonymous_variant 0.15
rpoB 762254 c.2448T>C synonymous_variant 0.14
rpoB 762257 c.2451C>G synonymous_variant 0.14
rpoC 763148 c.-222G>C upstream_gene_variant 0.13
rpoB 763161 p.Leu1119Ile missense_variant 0.14
rpoC 763483 c.114G>C synonymous_variant 0.12
rpoC 763486 c.117T>C synonymous_variant 0.14
rpoC 763570 c.201G>C synonymous_variant 0.17
rpoC 763573 c.204G>C synonymous_variant 0.17
rpoC 763741 c.372C>T synonymous_variant 0.17
rpoC 763744 c.375G>C synonymous_variant 0.16
rpoC 764791 c.1422C>G synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
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 1472148 n.303T>C non_coding_transcript_exon_variant 0.21
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.21
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.16
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.24
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.23
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.25
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.3
rrs 1472545 n.700A>G non_coding_transcript_exon_variant 0.12
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.2
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.2
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.2
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.32
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.27
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.28
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.23
rrs 1473062 n.1217T>G non_coding_transcript_exon_variant 0.12
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.12
rrl 1473871 n.214T>C non_coding_transcript_exon_variant 0.11
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.17
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.12
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.27
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.19
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.32
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.16
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.18
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.18
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.2
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.15
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.13
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.21
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.15
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.15
rrl 1475028 n.1371G>C non_coding_transcript_exon_variant 0.14
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.16
rrl 1475108 n.1451C>G non_coding_transcript_exon_variant 0.16
rrl 1475508 n.1851A>T non_coding_transcript_exon_variant 0.21
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.17
rrl 1475740 n.2083G>C non_coding_transcript_exon_variant 0.15
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.16
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.33
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.1
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rpsA 1834528 c.987T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067248 p.Thr233Ile missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039787 c.918G>C synonymous_variant 0.16
clpC1 4039790 c.915C>G synonymous_variant 0.16
clpC1 4039865 c.840T>C synonymous_variant 0.12
clpC1 4039875 p.Asn277Arg missense_variant 0.19
clpC1 4039886 c.819C>G synonymous_variant 0.18
clpC1 4039898 c.807C>G synonymous_variant 0.13
clpC1 4040117 c.588A>G synonymous_variant 0.11
clpC1 4040651 c.54A>G synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0