TB-Profiler result

Run: ERR2229536
Summary

Run ID: ERR2229536

Sample name:

Date: 31-03-2023 17:17:46

Number of reads: 1024613

Percentage reads mapped: 99.4

Strain: lineage4.8

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
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
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
fgd1 491316 c.534C>G synonymous_variant 0.12
mshA 576113 p.Arg256Gly missense_variant 0.67
rpoC 766397 p.Leu1010Met missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777167 c.1313delT frameshift_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781631 c.72G>T synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.11
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
inhA 1674403 p.Glu68* stop_gained 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102853 p.Ser64Pro missense_variant 0.11
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2167814 c.2799C>T synonymous_variant 0.17
PPE35 2168140 p.Ala825Thr missense_variant 0.19
PPE35 2168143 p.Phe824Leu missense_variant 0.19
PPE35 2168150 c.2463T>C synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289089 c.153C>T synonymous_variant 0.22
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.17
ribD 2986827 c.-12G>A upstream_gene_variant 0.15
Rv2752c 3064526 p.Ile556Phe missense_variant 0.12
Rv2752c 3065486 p.Ala236Ser missense_variant 0.15
fbiD 3339335 p.Ala73Gly missense_variant 0.17
whiB7 3568428 c.252A>G synonymous_variant 0.17
Rv3236c 3612980 p.Gly46Ala missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.16
clpC1 4039730 c.975C>G synonymous_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242839 p.Cys993Gly missense_variant 0.14
embA 4244537 c.1305T>C synonymous_variant 0.29
embA 4244544 p.Ala438Thr missense_variant 0.29
embA 4244732 c.1500G>T synonymous_variant 0.12
embA 4245433 p.Ala734Val missense_variant 0.18
embB 4246529 p.Ser6Arg missense_variant 0.27
embB 4246584 p.Arg24Pro missense_variant 0.43
aftB 4269225 c.-389C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0