TB-Profiler result

Run: ERR2229718
Summary

Run ID: ERR2229718

Sample name:

Date: 31-03-2023 17:29:02

Number of reads: 488700

Percentage reads mapped: 99.0

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 490611 c.-172T>C upstream_gene_variant 0.14
rpoB 760290 c.485delT frameshift_variant 0.15
rpoC 762659 c.-711C>A upstream_gene_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775640 c.2841C>G synonymous_variant 0.29
mmpL5 776854 p.Thr543Ser missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781556 c.-4G>T upstream_gene_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407235 c.104_105delTG frameshift_variant 0.25
Rv1258c 1407243 p.Leu33Gln missense_variant 0.25
embR 1416426 c.919_921delGCG conservative_inframe_deletion 0.15
embR 1416436 c.911_912insGTGGGT disruptive_inframe_insertion 0.14
embR 1416440 c.902_907delACCCAC disruptive_inframe_deletion 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475222 n.1565G>A non_coding_transcript_exon_variant 0.67
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.5
fabG1 1673349 c.-91G>C upstream_gene_variant 0.1
fabG1 1673357 c.-83G>A upstream_gene_variant 0.19
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
fabG1 1673713 p.Ser92Pro missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167695 p.Ile973Thr missense_variant 0.29
PPE35 2168506 p.Gly703Ser missense_variant 0.14
PPE35 2168518 p.Ile699Phe missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.22
PPE35 2169457 p.His386Asp missense_variant 0.12
PPE35 2169462 p.Val384Ala missense_variant 0.12
PPE35 2169748 p.Ile289Phe missense_variant 0.14
PPE35 2169749 c.864A>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.8
PPE35 2170053 p.Thr187Ser missense_variant 0.76
Rv1979c 2221783 p.Ala461Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289446 c.-205G>A upstream_gene_variant 0.14
kasA 2518402 c.288G>A synonymous_variant 0.15
eis 2715576 c.-244T>C upstream_gene_variant 0.25
folC 2747591 p.Ser3Leu missense_variant 0.2
pepQ 2860332 c.87C>T synonymous_variant 0.15
Rv2752c 3064570 p.Val541Ala missense_variant 0.29
Rv2752c 3066056 p.Gly46Ser missense_variant 0.33
thyX 3067602 p.Arg115Gln missense_variant 0.14
thyX 3067631 c.315C>A synonymous_variant 0.17
thyA 3073738 p.Asp245Val missense_variant 0.13
ald 3086768 c.-52G>T upstream_gene_variant 0.22
fbiD 3339372 c.255C>A synonymous_variant 0.13
fprA 3474708 p.Asp235Asn missense_variant 0.15
fbiB 3642787 p.Trp418* stop_gained 0.25
alr 3841146 p.Ala92Asp missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.22
clpC1 4039952 c.753T>C synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.42
embB 4246555 c.42G>C synonymous_variant 0.42
embB 4246556 p.Ala15Pro missense_variant 0.42
embB 4246722 p.Pro70Leu missense_variant 0.14
embB 4246747 p.Asp78Glu missense_variant 0.15
ethA 4326031 c.1443C>T synonymous_variant 0.17
ethA 4326836 p.Val213Ala 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