TB-Profiler result

Run: ERR2229086
Summary

Run ID: ERR2229086

Sample name:

Date: 31-03-2023 16:37:45

Number of reads: 1021867

Percentage reads mapped: 99.34

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
mshA 576456 p.Val370Gly missense_variant 0.25
mshA 576747 p.Gly467Asp missense_variant 0.12
ccsA 619841 c.-50C>A upstream_gene_variant 0.25
rpoC 765935 p.Ala856Ser missense_variant 0.14
rpoC 765943 p.Lys858Asn missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>A synonymous_variant 0.14
mmpL5 775718 c.2763C>G synonymous_variant 0.14
mmpL5 775726 c.2755C>T synonymous_variant 0.17
mmpL5 775727 c.2754C>G synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801194 p.Arg129Gln missense_variant 0.18
fbiC 1303398 c.468C>A synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303894 c.964C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.37
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102194 c.849T>C synonymous_variant 0.22
ndh 2102268 p.Val259Ile missense_variant 0.2
ndh 2102336 p.Leu236Ser missense_variant 0.17
PPE35 2167865 c.2748G>C synonymous_variant 0.2
PPE35 2167868 c.2745A>C synonymous_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.29
PPE35 2167967 c.2646A>C synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.16
PPE35 2169287 c.1326T>C synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.43
PPE35 2170065 p.Ala183Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518809 p.Lys232Arg missense_variant 0.21
kasA 2518864 c.750G>C synonymous_variant 0.16
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.15
eis 2714639 p.Asp232Tyr missense_variant 0.13
Rv2752c 3065766 p.Glu142Asp missense_variant 0.15
fbiD 3339315 c.198A>G synonymous_variant 0.12
whiB7 3568433 p.Arg83Cys missense_variant 0.22
Rv3236c 3612350 p.Ala256Val missense_variant 0.13
Rv3236c 3613083 p.Gly12Ser missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.29
ddn 3986833 c.-11G>T upstream_gene_variant 0.12
clpC1 4039042 p.Ser555Thr missense_variant 0.15
clpC1 4039566 p.Val380Gly missense_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.15
embC 4242047 p.Ser729Thr missense_variant 0.13
embC 4242522 p.Ala887Gly missense_variant 0.25
embA 4242526 c.-707C>G upstream_gene_variant 0.25
embC 4242591 p.His910Leu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242748 c.-485A>G upstream_gene_variant 0.18
embA 4244562 p.Arg444Gly missense_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.5
ubiA 4269529 p.Ala102Glu missense_variant 0.13
ethA 4326067 c.1407G>T synonymous_variant 0.15
ethR 4326961 c.-588G>C upstream_gene_variant 0.19
ethR 4326964 c.-585G>A upstream_gene_variant 0.19
ethR 4326970 c.-579G>T upstream_gene_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0