TB-Profiler result

Run: ERR2229104
Summary

Run ID: ERR2229104

Sample name:

Date: 31-03-2023 16:39:21

Number of reads: 742721

Percentage reads mapped: 99.36

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 491147 p.Trp122Leu missense_variant 0.11
mshA 575432 p.Gly29Ser missense_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576738 p.Val464Glu missense_variant 0.17
rpoB 761611 p.Gly602Glu missense_variant 0.11
rpoC 763616 p.Thr83Ser missense_variant 0.13
rpoC 763700 p.Pro111Ser missense_variant 0.14
rpoC 764341 c.972G>A synonymous_variant 0.12
rpoC 764980 c.1613dupG frameshift_variant 0.12
rpoC 767305 c.3936C>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304124 c.1194C>T synonymous_variant 0.4
atpE 1460997 c.-48T>C upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472873 n.1028C>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474131 n.474C>T non_coding_transcript_exon_variant 0.25
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.13
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167815 p.Tyr933Ser missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.62
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170309 p.Leu102Val missense_variant 0.17
Rv1979c 2222454 c.711G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518098 c.-17C>T upstream_gene_variant 0.12
kasA 2518198 p.Asp28Glu missense_variant 0.13
kasA 2518472 p.Glu120* stop_gained 0.14
ahpC 2725950 c.-243G>C upstream_gene_variant 0.14
folC 2746863 c.736C>T synonymous_variant 0.13
folC 2747264 p.Gly112Asp missense_variant 0.11
folC 2747321 p.Thr93Ile missense_variant 0.18
thyX 3067340 c.606G>A synonymous_variant 0.15
thyX 3067869 p.Thr26Ile missense_variant 0.12
ald 3086839 p.Thr7Ile missense_variant 0.14
fprA 3473871 c.-136G>A upstream_gene_variant 0.12
Rv3236c 3613091 p.Phe9Ser missense_variant 0.1
alr 3840989 c.432G>A synonymous_variant 0.22
clpC1 4039682 c.1023C>T synonymous_variant 0.17
clpC1 4039691 c.1014G>C synonymous_variant 0.17
clpC1 4039714 p.Tyr331His missense_variant 0.15
clpC1 4039730 c.975C>G synonymous_variant 0.17
clpC1 4039815 c.887_889delGAG disruptive_inframe_deletion 0.4
clpC1 4040144 c.561G>C synonymous_variant 0.13
embC 4239711 c.-152C>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242660 p.Leu933Pro missense_variant 0.14
embA 4243210 c.-23C>T upstream_gene_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.56
embB 4246548 p.Pro12Gln missense_variant 0.43
embB 4246555 c.42G>C synonymous_variant 0.43
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4246563 p.Leu17Trp missense_variant 0.43
embB 4246567 c.54G>T synonymous_variant 0.43
embB 4246890 p.Thr126Ile missense_variant 0.15
embB 4247028 p.Leu172Arg missense_variant 0.33
aftB 4268074 p.Ile255Val missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0