TB-Profiler result

Run: ERR2229132
Summary

Run ID: ERR2229132

Sample name:

Date: 31-03-2023 16:43:17

Number of reads: 880538

Percentage reads mapped: 69.87

Strain: lineage4.8

Drug-resistance: RR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761137 p.Thr444Ile missense_variant 0.13 rifampicin
thyA 3073990 p.Cys161Tyr missense_variant 0.14 para-aminosalicylic_acid
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 6245 p.Lys336* stop_gained 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 761758 p.Tyr651Cys missense_variant 0.12
rpoB 762095 p.Ile763Met missense_variant 0.12
rpoC 765261 p.Ala631Val missense_variant 0.45
rpoC 765575 p.Val736Leu missense_variant 0.14
rpoC 765591 p.Arg741His missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776393 c.2088C>T synonymous_variant 0.15
mmpR5 779478 p.Glu163Asp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406204 c.1137G>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473559 n.-99G>T upstream_gene_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475189 n.1532G>T non_coding_transcript_exon_variant 0.29
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.29
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.29
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.22
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.22
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.22
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.22
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.29
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.22
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.2
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
inhA 1674254 p.Asp18Val missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169377 p.Phe412Leu missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.37
Rv1979c 2222635 p.Phe177Ser missense_variant 0.12
Rv1979c 2222711 p.Asn152Tyr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518259 p.Glu49* stop_gained 0.14
kasA 2518879 c.765A>G synonymous_variant 0.12
kasA 2518882 c.768C>A synonymous_variant 0.12
ahpC 2725923 c.-270A>G upstream_gene_variant 0.12
ribD 2987244 p.Thr136Ser missense_variant 0.13
Rv2752c 3064990 p.Arg401Leu missense_variant 0.14
ald 3086670 c.-150G>A upstream_gene_variant 0.17
fbiD 3339582 c.465C>T synonymous_variant 0.12
fbiD 3339589 p.Leu158Val missense_variant 0.12
Rv3236c 3613099 c.18G>A synonymous_variant 0.13
fbiA 3641475 c.934delG frameshift_variant 0.12
clpC1 4039683 p.Arg341Leu missense_variant 0.14
clpC1 4039829 p.Leu292Ile missense_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246567 c.54_55insT frameshift_variant 0.2
embB 4246801 c.288G>T synonymous_variant 0.14
embB 4247272 c.759C>T synonymous_variant 0.14
embB 4247895 p.Pro461Arg missense_variant 0.11
embB 4249694 p.Trp1061Arg missense_variant 0.2
aftB 4267032 p.Ile602Thr missense_variant 0.15
aftB 4268272 p.Phe189Leu missense_variant 0.12
ethA 4326879 p.Ala199Thr missense_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethA 4327476 c.-3T>C upstream_gene_variant 0.12
ethR 4327715 p.Ile56Asn missense_variant 0.15
ethA 4328391 c.-918G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407786 c.417G>A synonymous_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0