TB-Profiler result

Run: ERR2229521

Summary

Run ID: ERR2229521

Sample name:

Date: 31-03-2023 17:16:47

Number of reads: 964184

Percentage reads mapped: 99.33

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 0.96
fgd1 491139 p.Glu119Asp missense_variant 0.12
mshA 575716 c.369C>T synonymous_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.43
mshA 576588 p.Gly414Val missense_variant 0.12
rpoC 765077 p.Ser570Thr missense_variant 0.12
rpoC 766218 p.Asp950Gly missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776023 p.Val820Leu missense_variant 0.17
mmpL5 776152 p.Met777Leu missense_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.17
mmpL5 777501 p.Thr327Asn missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416232 p.Cys372Gly missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.1
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474736 n.1084delG non_coding_transcript_exon_variant 0.11
rrl 1476656 n.2999G>C non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
rpsA 1834849 c.1308C>A synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918064 p.Pro42Leu missense_variant 0.15
tlyA 1918243 p.Asp102Asn missense_variant 0.13
katG 2154634 p.Asn493Ile missense_variant 0.11
katG 2155021 p.Ile364Asn missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169725 c.888T>C synonymous_variant 0.16
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.24
PPE35 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289448 c.-207G>T upstream_gene_variant 0.15
pncA 2289464 c.-223A>G upstream_gene_variant 0.13
kasA 2519057 p.Thr315Ser missense_variant 0.13
kasA 2519062 c.948T>G synonymous_variant 0.13
kasA 2519065 c.951C>A synonymous_variant 0.13
kasA 2519066 c.956_982delACGCCGCGGAGGCCAACGCCATCCGCG disruptive_inframe_deletion 0.25
kasA 2519129 p.Pro339Thr missense_variant 0.25
eis 2714323 p.Arg337His missense_variant 0.14
eis 2714350 p.Arg328Gln missense_variant 0.13
pepQ 2860154 p.Glu89Gln missense_variant 0.14
thyA 3073924 p.Leu183Ser missense_variant 0.1
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568431 c.249C>G synonymous_variant 0.23
Rv3236c 3612861 p.Leu86Val missense_variant 0.2
fbiA 3641452 p.Arg304Trp missense_variant 0.13
fbiB 3642436 p.Gln301Arg missense_variant 0.12
rpoA 3878013 p.Asp165Glu missense_variant 0.14
clpC1 4038773 p.Asp644Glu missense_variant 0.17
clpC1 4038776 p.Glu643Asp missense_variant 0.17
clpC1 4038782 c.1923G>C synonymous_variant 0.18
clpC1 4039691 c.1014G>C synonymous_variant 0.13
clpC1 4040057 c.648C>T synonymous_variant 0.14
embC 4242030 p.Leu723Pro missense_variant 0.11
embC 4242255 p.Pro798Gln missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.5
aftB 4267096 p.Pro581Ser missense_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.15
ethR 4328044 p.Leu166Met missense_variant 0.11
ethA 4328085 c.-612G>A upstream_gene_variant 0.11
whiB6 4338457 p.Thr22Lys missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0