TB-Profiler result

Run: ERR2229698
Summary

Run ID: ERR2229698

Sample name:

Date: 31-03-2023 17:27:12

Number of reads: 807575

Percentage reads mapped: 99.05

Strain: lineage4.8

Drug-resistance: RR-TB

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761092 p.Gln429Leu missense_variant 0.14 rifampicin
ethA 4327174 c.299delT frameshift_variant 0.14 ethionamide, ethionamide
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 6101 p.Glu288Lys missense_variant 0.14
gyrB 6488 p.Arg417Cys missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491133 c.351A>G synonymous_variant 0.18
mshA 575831 p.Gly162Arg missense_variant 0.18
ccsA 620477 p.Phe196Tyr missense_variant 0.12
ccsA 620537 p.Val216Glu missense_variant 0.12
rpoB 759872 c.66G>A synonymous_variant 0.29
rpoB 760259 p.Phe151Leu missense_variant 0.11
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 761240 c.1434C>T synonymous_variant 0.25
rpoB 762765 p.Leu987Met missense_variant 0.25
rpoC 764532 p.Gly388Ala missense_variant 0.33
rpoC 766310 p.Arg981Cys missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776216 c.2265G>A synonymous_variant 0.25
mmpL5 777457 p.Gly342Arg missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781699 p.Ser47Leu missense_variant 0.13
rplC 800712 c.-97A>G upstream_gene_variant 0.11
fbiC 1302875 c.-56C>A upstream_gene_variant 0.13
fbiC 1303038 c.108T>C synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304512 p.Val528Ile missense_variant 0.29
fbiC 1305203 c.2277delC frameshift_variant 0.11
Rv1258c 1406964 p.Ser126Leu missense_variant 0.12
embR 1416997 c.351C>A synonymous_variant 0.14
embR 1417229 p.Ala40Asp missense_variant 0.13
atpE 1461073 p.Leu10Pro missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471678 n.-168A>C upstream_gene_variant 0.12
rrs 1472163 n.318G>C non_coding_transcript_exon_variant 0.14
rrs 1472845 n.1000G>C non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474093 n.436G>C non_coding_transcript_exon_variant 0.14
rrl 1474277 n.620C>A non_coding_transcript_exon_variant 0.2
rrl 1474922 n.1265G>C non_coding_transcript_exon_variant 0.18
rrl 1475219 n.1562A>T non_coding_transcript_exon_variant 0.22
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
fabG1 1674056 p.Ile206Asn missense_variant 0.17
inhA 1674350 p.Ile50Thr missense_variant 0.29
inhA 1674623 p.Gly141Glu missense_variant 0.17
rpsA 1833392 c.-150C>A upstream_gene_variant 0.25
rpsA 1833932 p.Ile131Val missense_variant 0.14
tlyA 1917805 c.-135C>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.22
katG 2156350 c.-239C>T upstream_gene_variant 0.18
PPE35 2167865 c.2748G>C synonymous_variant 0.28
PPE35 2167868 c.2745A>C synonymous_variant 0.28
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2169614 c.999C>T synonymous_variant 0.13
PPE35 2169725 c.888T>C synonymous_variant 0.11
PPE35 2169739 c.859_873delTTCGGAATTGCGAAC conservative_inframe_deletion 0.17
PPE35 2169763 p.Ile284Phe missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.82
PPE35 2170053 p.Thr187Ser missense_variant 0.83
PPE35 2170088 c.525G>C synonymous_variant 0.11
PPE35 2170499 c.114A>G synonymous_variant 0.11
Rv1979c 2222281 p.Ile295Asn missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518492 p.Tyr126* stop_gained 0.18
kasA 2518516 c.402C>A synonymous_variant 0.17
kasA 2519153 p.Ile347Val missense_variant 0.18
kasA 2519167 c.1053T>C synonymous_variant 0.17
kasA 2519171 p.Leu353Val missense_variant 0.18
pepQ 2859423 c.996C>T synonymous_variant 0.18
thyX 3067340 c.606G>A synonymous_variant 0.18
thyA 3074580 c.-109T>C upstream_gene_variant 0.18
thyA 3074586 c.-115T>C upstream_gene_variant 0.2
ald 3087549 p.Ala244Ser missense_variant 0.17
fprA 3474143 p.Trp46Tyr missense_variant 0.21
alr 3841265 c.156G>T synonymous_variant 0.17
rpoA 3878163 c.345C>A synonymous_variant 0.14
rpoA 3878243 p.Glu89* stop_gained 0.12
clpC1 4038752 p.Gln651His missense_variant 0.15
clpC1 4039682 c.1023C>T synonymous_variant 0.12
clpC1 4039691 c.1014G>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245599 c.-915A>G upstream_gene_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.24
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.58
embB 4246556 p.Ala15Pro missense_variant 0.58
embB 4246563 p.Leu17Trp missense_variant 0.42
embB 4246567 c.54G>T synonymous_variant 0.29
embB 4246864 c.351C>T synonymous_variant 0.18
embB 4247028 p.Leu172Arg missense_variant 0.17
embB 4249730 c.3221delC frameshift_variant 0.18
ethA 4326221 p.Val418Asp missense_variant 0.14
ethA 4328146 c.-673G>A upstream_gene_variant 0.12
whiB6 4338417 c.105G>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0