TB-Profiler result

Run: ERR2229539
Summary

Run ID: ERR2229539

Sample name:

Date: 31-03-2023 17:17:41

Number of reads: 940165

Percentage reads mapped: 99.39

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
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576111 p.Ala255Gly missense_variant 0.29
rpoB 761152 p.Leu449Gln missense_variant 0.14
rpoC 766641 p.His1091Leu missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775871 c.2610C>T synonymous_variant 0.12
mmpL5 775939 p.Ala848Thr missense_variant 0.2
mmpL5 776004 p.Ile826Thr missense_variant 0.17
mmpL5 776660 c.1821C>A synonymous_variant 0.14
mmpL5 777338 p.Lys381Asn missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801115 p.Ala103Ser missense_variant 0.17
rplC 801201 c.393C>A synonymous_variant 0.15
fbiC 1303416 c.486C>A synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304670 c.1740G>T synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474537 n.880G>T non_coding_transcript_exon_variant 0.12
rrl 1475018 n.1361G>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
inhA 1673520 c.-682C>T upstream_gene_variant 0.15
inhA 1674313 p.Leu38Ile missense_variant 0.11
inhA 1674936 c.735G>T synonymous_variant 0.12
rpsA 1834267 p.Trp242Cys missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.27
PPE35 2169910 p.Asn235Tyr missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.58
PPE35 2170351 p.Thr88Ala missense_variant 0.11
PPE35 2170385 c.228G>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518494 c.382delC frameshift_variant 0.22
kasA 2518864 c.750G>C synonymous_variant 0.33
kasA 2518879 c.765A>G synonymous_variant 0.22
kasA 2518882 c.768C>A synonymous_variant 0.22
kasA 2519324 p.Phe404Leu missense_variant 0.14
folC 2746570 c.1029C>A synonymous_variant 0.15
pepQ 2859592 p.Ala276Glu missense_variant 0.12
thyX 3068002 c.-57C>A upstream_gene_variant 0.12
thyA 3074126 p.Leu116Met missense_variant 0.14
fbiD 3339734 p.Ala206Gly missense_variant 0.29
Rv3236c 3612118 c.999G>A synonymous_variant 0.15
fbiB 3642024 p.Ala164Ser missense_variant 0.15
fbiB 3642751 p.Asp406Val missense_variant 0.2
alr 3841021 p.Ser134Pro missense_variant 0.14
alr 3841203 p.Gly73Asp missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.23
clpC1 4038534 p.Arg724His missense_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.12
clpC1 4039989 p.Pro239His missense_variant 0.14
clpC1 4040010 p.Ala232Arg missense_variant 0.13
embC 4241541 p.Thr560Asn missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244701 p.Gly490Val missense_variant 0.13
embA 4244834 c.1602G>T synonymous_variant 0.14
embA 4244914 p.Leu561Gln missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246679 p.Leu56Ile missense_variant 0.33
embB 4246881 p.Val123Gly missense_variant 0.13
embB 4249004 c.2492delT frameshift_variant 0.12
aftB 4268712 p.Leu42Ser missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0