TB-Profiler result

Run: ERR2229440
Summary

Run ID: ERR2229440

Sample name:

Date: 31-03-2023 17:11:43

Number of reads: 817108

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 491402 p.Leu207Pro missense_variant 0.2
mshA 575545 c.198C>T synonymous_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.5
mshA 576111 p.Ala255Gly missense_variant 0.22
mshA 576488 p.Val381His missense_variant 0.15
rpoB 759711 c.-96G>A upstream_gene_variant 0.13
rpoC 766354 c.2985C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303663 c.733C>T synonymous_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303886 p.Ala319Glu missense_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
rpsA 1833954 p.Leu138Gln missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.16
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.19
PPE35 2170238 c.375T>G synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519041 c.927C>T synonymous_variant 0.18
fprA 3474144 p.Trp46Cys missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.17
clpC1 4039031 c.1674T>C synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244677 p.Ser482* stop_gained 0.18
embB 4246544 p.Thr11Pro missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246696 c.183G>T synonymous_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4247394 p.Gly294Ala missense_variant 0.11
aftB 4268628 p.Gly70Val missense_variant 0.29
aftB 4269114 c.-278C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407677 p.Arg176Cys missense_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0