TB-Profiler result

Run: ERR2229385
Summary

Run ID: ERR2229385

Sample name:

Date: 31-03-2023 17:09:07

Number of reads: 1011002

Percentage reads mapped: 98.92

Strain: lineage4.8

Drug-resistance: Other

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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
mmpR5 779178 p.Ser63Arg missense_variant 0.11 clofazimine, bedaquiline
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 8681 c.1380C>A synonymous_variant 0.14
mshA 576701 p.Arg452Cys missense_variant 0.33
ccsA 620086 p.Asp66Asn missense_variant 0.13
ccsA 620862 c.972C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775927 c.2554C>T synonymous_variant 0.14
mmpL5 776366 c.2115G>A synonymous_variant 0.13
mmpL5 776840 c.1641C>T synonymous_variant 0.22
mmpS5 778602 c.303delC frameshift_variant 0.13
mmpL5 779203 c.-723G>T upstream_gene_variant 0.12
mmpS5 779667 c.-762A>G upstream_gene_variant 0.12
rpsL 781361 c.-199G>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800968 p.Tyr54Asp missense_variant 0.12
fbiC 1303663 c.733C>T synonymous_variant 0.29
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304426 p.Leu499Pro missense_variant 0.12
Rv1258c 1406339 p.Tyr334* stop_gained 0.18
embR 1416517 c.831C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471873 n.28C>G non_coding_transcript_exon_variant 0.2
rrs 1471908 n.63A>G non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474484 n.827C>G non_coding_transcript_exon_variant 0.18
rrl 1476099 n.2442A>T non_coding_transcript_exon_variant 0.33
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 c.2868C>G synonymous_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169169 c.1444T>C synonymous_variant 0.14
PPE35 2169170 c.1443C>G synonymous_variant 0.12
PPE35 2169176 c.1437G>A synonymous_variant 0.13
PPE35 2169179 c.1434C>G synonymous_variant 0.13
PPE35 2169191 c.1422G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.77
PPE35 2170053 p.Thr187Ser missense_variant 0.78
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518333 c.219C>T synonymous_variant 0.12
kasA 2518864 c.750G>C synonymous_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.29
kasA 2519143 c.1029G>C synonymous_variant 0.29
kasA 2519153 p.Ile347Val missense_variant 0.2
pepQ 2859799 p.Pro207Gln missense_variant 0.12
pepQ 2860157 p.Gly88Arg missense_variant 0.18
pepQ 2860460 c.-42G>T upstream_gene_variant 0.11
ribD 2987509 c.672delG frameshift_variant 0.12
thyX 3068011 c.-66C>T upstream_gene_variant 0.13
thyX 3068015 c.-70T>G upstream_gene_variant 0.13
thyX 3068028 c.-83G>A upstream_gene_variant 0.15
Rv3083 3448317 c.-187G>A upstream_gene_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612170 p.Glu316Val missense_variant 0.29
fbiB 3642177 p.Ala215Thr missense_variant 0.13
fbiB 3642365 p.Glu277Asp missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.13
rpoA 3878356 p.Val51Asp missense_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245857 c.-657C>T upstream_gene_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.32
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.53
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4247024 p.Pro171Ala missense_variant 0.29
aftB 4268617 p.Gly74Cys missense_variant 0.25
ethR 4326778 c.-771G>A upstream_gene_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