TB-Profiler result

Run: ERR2229054
Summary

Run ID: ERR2229054

Sample name:

Date: 31-03-2023 16:33:38

Number of reads: 1023433

Percentage reads mapped: 99.47

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
mshA 575575 c.228G>T synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.26
rpoC 764603 p.Arg412Trp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775778 c.2703C>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303306 p.Asp126Tyr missense_variant 0.17
fbiC 1303593 c.663G>T synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406444 c.896delG frameshift_variant 0.13
Rv1258c 1406511 p.Gly277Val missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.37
inhA 1674747 c.546C>T synonymous_variant 0.14
rpsA 1834018 c.477C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102305 c.738T>C synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.34
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289168 p.Ala25Asp missense_variant 0.12
pncA 2289627 c.-386C>T upstream_gene_variant 0.12
kasA 2518388 p.Gly92* stop_gained 0.14
ahpC 2725938 c.-255_-254insA upstream_gene_variant 0.15
folC 2747014 c.585C>A synonymous_variant 0.13
pepQ 2859580 p.Leu280Pro missense_variant 0.13
pepQ 2860105 p.Asp105Gly missense_variant 0.13
thyX 3067340 c.606G>A synonymous_variant 0.25
fbiD 3339496 p.Glu127Lys missense_variant 0.12
fprA 3474122 c.118delG frameshift_variant 0.12
fprA 3474566 p.Arg187Leu missense_variant 0.11
Rv3236c 3612789 p.Leu110Phe missense_variant 0.12
fbiB 3642199 p.Val222Ala missense_variant 0.25
fbiB 3642261 p.Leu243Phe missense_variant 0.18
fbiB 3642323 c.792_794delCCG disruptive_inframe_deletion 0.18
clpC1 4040057 c.648C>T synonymous_variant 0.18
clpC1 4040434 p.Ser91Gly missense_variant 0.12
panD 4044046 p.Val79Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243946 c.714C>G synonymous_variant 0.17
embA 4244438 c.1206C>G synonymous_variant 0.1
embA 4244659 p.Leu476Pro missense_variant 0.12
embA 4244858 c.1626G>T synonymous_variant 0.17
embA 4245789 p.Thr853Ser missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.21
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.18
ubiA 4269058 p.Ile259Thr missense_variant 0.12
ethA 4327506 c.-33A>T upstream_gene_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