TB-Profiler result

Run: ERR1750880
Summary

Run ID: ERR1750880

Sample name:

Date: 31-03-2023 14:58:24

Number of reads: 9239802

Percentage reads mapped: 96.5

Strain: lineage4.4.1.1.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans 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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 9304 p.Gly668Asp missense_variant 0.99
rpoC 766487 p.Pro1040Ser missense_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 1472150 n.305T>A non_coding_transcript_exon_variant 0.23
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.32
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.22
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.19
rrl 1474000 n.343C>G non_coding_transcript_exon_variant 0.15
rrl 1474065 n.408C>T non_coding_transcript_exon_variant 0.12
rrl 1474612 n.955T>C non_coding_transcript_exon_variant 0.11
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.15
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.14
rrl 1475341 n.1684C>G non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.12
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.17
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.12
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.11
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.12
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.12
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.12
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.2
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.25
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>C non_coding_transcript_exon_variant 0.22
rrl 1476383 n.2726T>C non_coding_transcript_exon_variant 0.2
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.14
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.17
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.31
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
rrl 1476522 n.2865G>A non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.99
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064993 p.Trp400* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339287 p.Arg57Leu missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 0.99
ubiA 4269671 p.Val55Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0