TB-Profiler result

Run: ERR2229497
Summary

Run ID: ERR2229497

Sample name:

Date: 31-03-2023 17:16:11

Number of reads: 761473

Percentage reads mapped: 99.12

Strain: lineage4.8

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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 491249 p.Arg156Gln missense_variant 0.18
fgd1 491275 p.Val165Leu missense_variant 0.25
fgd1 491377 p.Gly199Cys missense_variant 0.5
mshA 576108 p.Ala254Gly missense_variant 0.42
ccsA 619964 p.Leu25Pro missense_variant 0.12
rpoB 760586 c.780C>T synonymous_variant 0.17
rpoC 764001 p.Arg211Pro missense_variant 0.14
rpoC 764401 c.1032C>T synonymous_variant 0.13
rpoC 766326 p.Gly986Asp missense_variant 0.17
rpoC 766402 c.3033C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801155 p.Gly116Ala missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406367 p.Tyr325Ser missense_variant 0.12
embR 1416612 p.Thr246Ser missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472183 n.338C>A non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476615 n.2958T>C non_coding_transcript_exon_variant 0.18
fabG1 1673346 c.-94C>G upstream_gene_variant 0.19
fabG1 1673349 c.-91G>C upstream_gene_variant 0.19
fabG1 1673357 c.-83G>A upstream_gene_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.17
fabG1 1673361 c.-79C>G upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.38
rpsA 1833775 p.Glu78Asp missense_variant 0.15
rpsA 1834311 c.772delG frameshift_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918412 p.Ile158Thr missense_variant 0.18
ndh 2102638 c.405A>G synonymous_variant 0.17
katG 2154534 c.1578G>A synonymous_variant 0.18
PPE35 2167865 c.2748G>C synonymous_variant 0.24
PPE35 2167868 c.2745A>C synonymous_variant 0.24
PPE35 2168220 p.Ala798Glu missense_variant 0.33
PPE35 2168337 p.Leu759Ser missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169125 p.Val496Ile missense_variant 0.25
PPE35 2169269 c.1344A>G synonymous_variant 0.19
PPE35 2169272 c.1341C>G synonymous_variant 0.2
PPE35 2169278 c.1335T>C synonymous_variant 0.21
PPE35 2169281 c.1332T>G synonymous_variant 0.21
PPE35 2169287 c.1326T>C synonymous_variant 0.19
PPE35 2169293 c.1320T>C synonymous_variant 0.14
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170400 c.213G>C synonymous_variant 0.12
Rv1979c 2222245 p.Gly307Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518649 p.Ala179Ser missense_variant 0.2
ahpC 2726284 p.Pro31Leu missense_variant 0.17
folC 2747653 c.-56delC upstream_gene_variant 0.4
thyX 3068011 c.-66C>T upstream_gene_variant 0.14
thyX 3068015 c.-70T>G upstream_gene_variant 0.14
thyX 3068129 c.-184A>T upstream_gene_variant 0.5
thyA 3074571 c.-100T>C upstream_gene_variant 0.15
thyA 3074579 c.-108G>A upstream_gene_variant 0.17
thyA 3074580 c.-109T>C upstream_gene_variant 0.17
thyA 3074586 c.-115T>C upstream_gene_variant 0.18
fbiD 3339218 p.Thr34Ile missense_variant 0.14
Rv3236c 3613057 c.60G>T synonymous_variant 0.25
fbiB 3641714 c.180G>A synonymous_variant 0.14
alr 3840479 c.942C>T synonymous_variant 0.2
rpoA 3877758 c.750G>T synonymous_variant 0.13
rpoA 3877956 p.Glu184Asp missense_variant 0.18
rpoA 3877962 c.546G>T synonymous_variant 0.18
rpoA 3878238 c.270C>T synonymous_variant 0.22
rpoA 3878487 c.21C>A synonymous_variant 0.2
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4038181 p.Gly842Ser missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244620 p.Leu463Ser missense_variant 0.29
embB 4246544 p.Thr11Pro missense_variant 0.38
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 4247426 p.Gly305Thr missense_variant 0.17
embB 4247678 c.1166delT frameshift_variant 0.18
embB 4248363 p.Ser617Leu missense_variant 0.15
embB 4248683 p.Ala724Thr missense_variant 0.22
aftB 4267033 p.Ile602Val missense_variant 0.29
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethR 4327571 p.Gln8Arg missense_variant 0.17
ethA 4328453 c.-980T>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0