TB-Profiler result

Run: ERR2229078
Summary

Run ID: ERR2229078

Sample name:

Date: 31-03-2023 16:36:08

Number of reads: 560698

Percentage reads mapped: 99.38

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 6174 p.Glu312Val missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7558 p.Pro86Leu missense_variant 0.17
rpoB 759624 c.-183G>T upstream_gene_variant 0.17
rpoB 760571 c.765G>A synonymous_variant 0.13
rpoC 764541 p.Val391Asp missense_variant 0.22
rpoC 767042 p.Ser1225Ala missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781562 c.3G>T start_lost 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474752 n.1095T>C non_coding_transcript_exon_variant 0.2
rrl 1475487 n.1830C>A non_coding_transcript_exon_variant 0.17
rrl 1476201 n.2544C>A non_coding_transcript_exon_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
fabG1 1673414 c.-26C>A upstream_gene_variant 0.14
rpsA 1833831 c.293delG frameshift_variant 0.12
rpsA 1834762 c.1221C>T synonymous_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918198 p.Leu87Met missense_variant 0.17
ndh 2102389 c.654G>C synonymous_variant 0.18
ndh 2102392 c.651C>A synonymous_variant 0.18
ndh 2102569 c.474C>T synonymous_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.15
PPE35 2167833 p.Leu927Arg missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.4
PPE35 2170157 p.Ala152Ser missense_variant 0.26
PPE35 2170595 c.18G>A synonymous_variant 0.13
Rv1979c 2222421 c.744G>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518321 p.Asp69Glu missense_variant 0.17
eis 2715039 c.294C>T synonymous_variant 0.15
folC 2746660 c.939C>T synonymous_variant 0.14
ribD 2986847 p.Asp3Glu missense_variant 0.14
ribD 2987187 p.Leu117Met missense_variant 0.18
fbiA 3640355 c.-188C>A upstream_gene_variant 0.12
fbiA 3640486 c.-57G>T upstream_gene_variant 0.15
fbiB 3641395 c.-140C>T upstream_gene_variant 0.13
fbiB 3642707 c.1173C>A synonymous_variant 0.2
fbiB 3642719 p.Ser395Arg missense_variant 0.17
clpC1 4038169 c.2531_2535delAGCCG frameshift_variant 0.17
clpC1 4038178 c.2526_2527insT frameshift_variant 0.15
clpC1 4038183 p.Gly841Ala missense_variant 0.15
clpC1 4038446 c.2259T>C synonymous_variant 0.22
clpC1 4039682 c.1023C>T synonymous_variant 0.18
clpC1 4039691 c.1014G>C synonymous_variant 0.17
panD 4044075 c.207T>C synonymous_variant 0.14
panD 4044244 p.Ala13Asp missense_variant 0.22
embC 4240801 c.939C>T synonymous_variant 0.15
embC 4240803 p.Tyr314Phe missense_variant 0.15
embC 4241097 c.1238_1240delTGG disruptive_inframe_deletion 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243814 c.585delT frameshift_variant 0.17
embB 4246487 c.-27T>C upstream_gene_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246567 c.54_55insT frameshift_variant 0.5
embB 4247026 c.513G>C synonymous_variant 0.2
embB 4248301 p.Phe596Leu missense_variant 0.12
aftB 4267687 p.Gly384Cys missense_variant 0.12
ethR 4327835 p.Asp96Val missense_variant 0.14
ethA 4328031 c.-558C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0