TB-Profiler result

Run: ERR2228796
Summary

Run ID: ERR2228796

Sample name:

Date: 31-03-2023 16:21:10

Number of reads: 806986

Percentage reads mapped: 99.34

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 5962 c.723T>A synonymous_variant 0.33
gyrB 6012 p.Val258Gly missense_variant 0.25
gyrB 6040 c.801C>T synonymous_variant 0.17
gyrB 6286 p.Asp349Glu missense_variant 0.18
gyrB 6542 p.Ile435Leu missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490892 p.Val37Gly missense_variant 0.2
rpoB 760925 c.1119T>G synonymous_variant 0.21
rpoB 761665 p.Val620Gly missense_variant 0.17
rpoC 766665 p.Leu1099Arg missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303516 p.Met196Val missense_variant 0.2
fbiC 1303670 p.Asp247Ala missense_variant 0.29
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304840 p.Glu637Gly missense_variant 0.17
Rv1258c 1406230 p.Thr371Pro missense_variant 0.36
embR 1417015 p.Asp111Glu missense_variant 0.2
embR 1417085 p.Ile88Ser missense_variant 0.33
atpE 1461109 p.Ile22Ser missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472421 n.576G>A non_coding_transcript_exon_variant 0.33
rrs 1472434 n.589T>G non_coding_transcript_exon_variant 0.43
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834907 p.Ser456Ala missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167678 p.Gly979Cys missense_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169328 p.Asn429Tyr missense_variant 0.18
PPE35 2169547 p.His356Tyr missense_variant 0.18
PPE35 2170019 p.Phe198Leu missense_variant 0.18
PPE35 2170029 p.Met195Arg missense_variant 0.22
PPE35 2170466 c.147A>C synonymous_variant 0.18
Rv1979c 2221888 p.Val426Gly missense_variant 0.33
Rv1979c 2222651 p.Phe172Ile missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289507 c.-266A>T upstream_gene_variant 0.29
pncA 2290144 c.-903A>T upstream_gene_variant 0.4
kasA 2518020 c.-95A>G upstream_gene_variant 0.15
eis 2714725 p.Glu203Ala missense_variant 0.17
ahpC 2725946 c.-247A>C upstream_gene_variant 0.29
ahpC 2726731 p.Lys180Met missense_variant 0.33
ahpC 2726777 c.585C>A synonymous_variant 0.14
folC 2747612 c.-14T>G upstream_gene_variant 0.23
folC 2747673 c.-75T>A upstream_gene_variant 0.33
pepQ 2859639 c.780T>G synonymous_variant 0.21
Rv2752c 3064566 c.1626G>C synonymous_variant 0.29
Rv2752c 3066094 p.Val33Asp missense_variant 0.29
thyX 3067390 p.Thr186Pro missense_variant 0.22
thyX 3067461 p.Leu162Gln missense_variant 0.27
fbiD 3339686 p.Asp190Ala missense_variant 0.19
Rv3236c 3613048 c.69A>T synonymous_variant 0.75
Rv3236c 3613261 c.-145T>G upstream_gene_variant 0.47
fbiA 3640445 c.-98A>T upstream_gene_variant 0.5
fbiB 3642216 p.Thr228Pro missense_variant 0.23
clpC1 4038798 p.Asn636Thr missense_variant 0.18
embC 4242245 p.Thr795Pro missense_variant 0.29
embC 4242284 p.Phe808Ile missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244839 p.Leu536Arg missense_variant 0.33
embA 4244854 p.Val541Ala missense_variant 0.33
embA 4245469 p.Asn746Ile missense_variant 0.2
embB 4245545 c.-969C>A upstream_gene_variant 0.17
embA 4245688 p.Val819Gly missense_variant 0.2
embA 4246042 p.Asp937Ala missense_variant 0.17
aftB 4267029 p.Asp603Ala missense_variant 0.45
aftB 4267950 p.Pro296His missense_variant 0.14
aftB 4268239 p.Met200Leu missense_variant 0.18
aftB 4268709 p.Ala43Gly missense_variant 0.18
aftB 4268920 c.-84A>T upstream_gene_variant 0.38
ethR 4328045 p.Leu166Gln missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407649 p.Asp185Gly missense_variant 0.12
Rv3083 3448500 c.-3_*1408del transcript_ablation 1.0