TB-Profiler result

Run: ERR2229293
Summary

Run ID: ERR2229293

Sample name:

Date: 31-03-2023 16:58:11

Number of reads: 1262869

Percentage reads mapped: 99.11

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 491497 p.Pro239Thr missense_variant 0.12
mshA 575277 c.-71A>G upstream_gene_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.4
rpoC 764367 p.Gly333Asp missense_variant 0.11
rpoC 764541 p.Val391Gly missense_variant 0.2
rpoC 764543 p.Thr392Asp missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775813 p.Phe890Val missense_variant 0.15
mmpL5 775817 c.2664T>C synonymous_variant 0.18
mmpL5 775820 c.2661G>A synonymous_variant 0.18
mmpL5 777164 c.1317C>T synonymous_variant 0.16
mmpL5 777607 p.Gly292Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
fabG1 1673560 p.Lys41Gln missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102376 p.Pro223Ser missense_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.2
PPE35 2167865 c.2748G>C synonymous_variant 0.13
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2167973 c.2640A>G synonymous_variant 0.14
PPE35 2168027 c.2586C>T synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.32
PPE35 2169910 p.Asn235Tyr missense_variant 0.34
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.13
kasA 2518882 c.768C>A synonymous_variant 0.13
folC 2746992 p.Asp203Asn missense_variant 0.12
fbiD 3339744 c.627A>C synonymous_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.29
clpC1 4039645 p.His354Asp missense_variant 0.14
embC 4242069 p.Val736Ala missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242854 p.Gly998Ser missense_variant 0.12
embA 4244668 p.Val479Ala missense_variant 0.1
embB 4246555 c.42G>C synonymous_variant 0.15
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246567 c.54G>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0