TB-Profiler result

Run: ERR2229178
Summary

Run ID: ERR2229178

Sample name:

Date: 31-03-2023 16:47:32

Number of reads: 869024

Percentage reads mapped: 99.08

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 6689 p.Lys484Glu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491142 c.360C>T synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576513 p.Leu389Gln missense_variant 0.4
rpoB 762733 p.Glu976Val missense_variant 0.18
rpoB 762870 p.Met1022Val missense_variant 0.11
rpoC 763730 c.365delC frameshift_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776017 p.Ile822Leu missense_variant 0.12
mmpL5 776728 p.Phe585Leu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416963 c.384delC frameshift_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.12
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.12
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.1
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.11
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.11
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.11
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.38
inhA 1674394 p.Val65Leu missense_variant 0.29
inhA 1674699 p.Ser166Arg missense_variant 0.14
rpsA 1834052 p.Ala171Ser missense_variant 0.17
rpsA 1834345 p.Asp268Glu missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102148 c.895C>A synonymous_variant 0.14
katG 2155294 p.Gly273Val missense_variant 0.2
PPE35 2167773 p.Gly947Val missense_variant 0.22
PPE35 2167833 p.Leu927Arg missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169890 c.723C>T synonymous_variant 0.16
PPE35 2169893 c.720C>A synonymous_variant 0.16
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170053 p.Thr187Ser missense_variant 0.15
PPE35 2170159 p.Ala152Ser missense_variant 0.21
PPE35 2170381 p.Ala78Ser missense_variant 0.15
PPE35 2170382 p.Ala77Gly missense_variant 0.14
PPE35 2170387 c.226C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289714 c.-473G>T upstream_gene_variant 0.17
kasA 2518348 c.234A>T synonymous_variant 0.12
kasA 2518486 c.372G>A synonymous_variant 0.2
kasA 2518723 c.609G>A synonymous_variant 0.33
thyX 3067340 c.606G>A synonymous_variant 0.13
thyX 3067800 p.Lys49Thr missense_variant 0.14
Rv3236c 3612286 c.831A>G synonymous_variant 0.17
fbiB 3640563 c.-972C>T upstream_gene_variant 0.14
fbiB 3642232 c.700_701delCG frameshift_variant 0.13
clpC1 4039355 c.1350G>T synonymous_variant 0.11
panD 4043926 p.His119Leu missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.29
ubiA 4269001 p.Ala278Val missense_variant 0.13
ubiA 4269446 p.Val130Ile missense_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