TB-Profiler result

Run: ERR2229512
Summary

Run ID: ERR2229512

Sample name:

Date: 31-03-2023 17:16:34

Number of reads: 735257

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
gyrB 6536 p.Thr433Ser missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8561 c.1260A>T synonymous_variant 0.11
fgd1 490933 p.Ala51Ser missense_variant 0.13
fgd1 491705 p.Leu308Pro missense_variant 0.13
mshA 575161 c.-187T>C upstream_gene_variant 0.12
ccsA 620559 p.Gln223His missense_variant 0.13
rpoB 761031 p.Gln409Glu missense_variant 0.25
rpoB 763258 p.Arg1151Leu missense_variant 0.13
rpoC 763575 p.Arg69His missense_variant 0.12
rpoC 763704 p.Ser112Leu missense_variant 0.11
rpoC 765443 p.Val692Met missense_variant 0.2
rpoC 765452 p.Ala695Ser missense_variant 0.25
rpoC 765817 c.2448G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775947 p.Ala845Asp missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406192 p.Leu383Phe missense_variant 0.12
embR 1416433 c.915C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472752 n.907A>G non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474859 n.1202A>T non_coding_transcript_exon_variant 0.15
rrl 1475729 n.2072C>T non_coding_transcript_exon_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
inhA 1673592 c.-610G>T upstream_gene_variant 0.22
inhA 1673850 c.-352C>T upstream_gene_variant 0.14
tlyA 1917785 c.-155C>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918670 p.Arg244His missense_variant 0.12
ndh 2102106 p.Gly313Trp missense_variant 0.25
ndh 2102661 p.Asn128Asp missense_variant 0.15
PPE35 2167763 p.Ile950Val missense_variant 0.11
PPE35 2168071 p.Glu848* stop_gained 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.11
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169902 p.Leu237Phe missense_variant 0.24
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.62
PPE35 2170147 p.Ser156Ala missense_variant 0.18
PPE35 2170159 p.Ala152Ser missense_variant 0.11
Rv1979c 2222354 p.Leu271Ile missense_variant 0.18
Rv1979c 2222506 p.Ser220Ile missense_variant 0.11
Rv1979c 2223024 c.141G>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714340 c.993C>A synonymous_variant 0.12
eis 2714675 p.Pro220Ser missense_variant 0.15
folC 2746822 c.777G>A synonymous_variant 0.25
pepQ 2860154 p.Glu89Gln missense_variant 0.2
Rv2752c 3064588 p.Arg535His missense_variant 0.17
fprA 3474822 c.816G>A synonymous_variant 0.12
whiB7 3568415 p.Asp89Tyr missense_variant 0.17
whiB7 3568774 c.-95G>C upstream_gene_variant 0.14
fbiA 3641233 p.Ala231Thr missense_variant 0.2
fbiB 3641979 p.Thr149Pro missense_variant 0.18
fbiB 3642601 p.Gly356Val missense_variant 0.12
rpoA 3877982 p.Tyr176His missense_variant 0.12
ddn 3986826 c.-18G>C upstream_gene_variant 0.13
clpC1 4038491 c.2214C>G synonymous_variant 0.12
clpC1 4038542 p.Gln721His missense_variant 0.11
embC 4240422 p.Glu187Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242801 p.Pro980Arg missense_variant 0.11
embA 4245025 p.His598Arg missense_variant 0.1
embA 4245275 c.2043C>A synonymous_variant 0.12
embA 4246218 p.His996Tyr missense_variant 0.12
embA 4246392 p.Trp1054Arg missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
aftB 4268620 p.Val73Leu missense_variant 0.25
aftB 4268872 c.-36G>T upstream_gene_variant 0.17
ethR 4327562 p.Ala5Glu missense_variant 0.11
ethR 4327778 p.Asp77Ala missense_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