TB-Profiler result

Run: ERR2229446
Summary

Run ID: ERR2229446

Sample name:

Date: 31-03-2023 17:11:55

Number of reads: 533547

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490614 c.-169A>G upstream_gene_variant 0.11
mshA 575732 p.Leu129Ile missense_variant 0.15
mshA 575962 p.Gln205His missense_variant 0.15
ccsA 620266 p.Ala126Ser missense_variant 0.17
rpoB 762215 p.Lys803Asn missense_variant 0.29
rpoC 766442 p.Thr1025Ser missense_variant 0.22
rpoC 766930 c.3561G>A synonymous_variant 0.14
rpoC 767069 p.Thr1234Ser missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777164 c.1317C>T synonymous_variant 0.2
mmpS5 778626 c.279_280insGTGAGCG frameshift_variant 0.18
mmpS5 778630 p.Leu92Ser missense_variant 0.18
mmpS5 778632 c.267_273delGCTCACC frameshift_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302952 p.Lys8Glu missense_variant 0.12
fbiC 1303058 p.Glu43Gly missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304563 p.Thr545Pro missense_variant 0.13
Rv1258c 1406461 p.Ala294Thr missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476330 n.2673A>T non_coding_transcript_exon_variant 0.13
rrl 1476553 n.2896C>A non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
inhA 1674889 p.Trp230Arg missense_variant 0.14
rpsA 1834372 c.831G>A synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101995 p.Glu350Gln missense_variant 0.12
ndh 2102279 p.Asn255Thr missense_variant 0.2
katG 2153970 p.Asp714Glu missense_variant 0.13
katG 2154715 p.Gly466Val missense_variant 0.13
PPE35 2168150 c.2463T>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.29
PPE35 2170157 c.456G>C synonymous_variant 0.12
PPE35 2170385 c.228G>T synonymous_variant 0.14
PPE35 2170392 p.Gly74Ala missense_variant 0.15
PPE35 2170403 c.210C>A synonymous_variant 0.15
PPE35 2170406 c.207A>G synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290101 c.-860T>C upstream_gene_variant 0.25
kasA 2518593 p.Ala160Gly missense_variant 0.25
eis 2715155 p.Gly60Arg missense_variant 0.12
folC 2746928 p.Pro224His missense_variant 0.25
ribD 2987357 c.519C>A synonymous_variant 0.22
thyA 3073914 c.558C>T synonymous_variant 0.17
Rv3236c 3613001 p.Ala39Val missense_variant 0.13
Rv3236c 3613197 c.-81G>A upstream_gene_variant 0.12
fbiB 3642313 p.Arg260His missense_variant 0.33
fbiB 3642692 c.1158C>A synonymous_variant 0.17
rpoA 3877765 p.Ala248Val missense_variant 0.2
clpC1 4038304 p.Thr801Ala missense_variant 0.2
clpC1 4040144 c.561G>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244729 p.Phe499Leu missense_variant 0.2
embB 4246469 c.-45C>A upstream_gene_variant 0.17
embB 4247615 p.Glu368* stop_gained 0.2
embB 4247969 p.Gly486Ser missense_variant 0.14
aftB 4267900 p.Ala313Ser missense_variant 0.25
ubiA 4269238 p.Ala199Asp missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0