TB-Profiler result

Run: ERR2229346

Summary

Run ID: ERR2229346

Sample name:

Date: 31-03-2023 17:05:08

Number of reads: 1206860

Percentage reads mapped: 96.96

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 491194 p.Leu138Ile missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576111 p.Ala255Gly missense_variant 0.22
rpoB 759988 p.Ser61Leu missense_variant 0.14
rpoB 760025 p.Asp73Glu missense_variant 0.14
rpoB 760400 c.594G>T synonymous_variant 0.14
rpoB 763010 p.Trp1068* stop_gained 0.12
rpoC 764399 p.Tyr344His missense_variant 0.11
rpoC 765944 p.Gly859Ser missense_variant 0.12
rpoC 766532 p.Leu1055Ile missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778086 c.394delG frameshift_variant 0.12
mmpL5 779157 c.-677C>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781754 c.195G>A synonymous_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407439 c.-99G>A upstream_gene_variant 0.12
Rv1258c 1407518 c.-178C>G upstream_gene_variant 0.15
embR 1416763 c.584delA frameshift_variant 0.17
embR 1417191 p.Asp53Asn missense_variant 0.15
atpE 1460889 c.-156T>A upstream_gene_variant 0.25
atpE 1460917 c.-128C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474494 n.837C>A non_coding_transcript_exon_variant 0.12
rrl 1475421 n.1764C>A non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.2
fabG1 1673349 c.-91G>C upstream_gene_variant 0.21
fabG1 1673357 c.-83G>A upstream_gene_variant 0.25
fabG1 1673359 c.-81T>C upstream_gene_variant 0.27
fabG1 1673361 c.-79C>G upstream_gene_variant 0.27
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
tlyA 1917927 c.-13G>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154976 p.Ala379Asp missense_variant 0.14
PPE35 2167814 c.2799C>T synonymous_variant 0.14
PPE35 2168047 p.Leu856Val missense_variant 0.12
PPE35 2168090 p.Ile841Met missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169146 c.1467G>C synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.68
PPE35 2170557 p.Ala19Val missense_variant 0.13
Rv1979c 2222219 p.Asn316Asp missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289189 p.Ser18Leu missense_variant 0.14
kasA 2518879 c.765A>G synonymous_variant 0.12
ahpC 2726099 c.-93delG upstream_gene_variant 0.13
folC 2746590 p.Gly337Ser missense_variant 0.25
folC 2746931 p.Ala223Asp missense_variant 0.13
folC 2746976 p.Asp208Gly missense_variant 0.11
thyX 3067533 p.Ala138Gly missense_variant 0.13
thyX 3067537 c.408_409insA frameshift_variant 0.15
fbiD 3339214 p.Gln33* stop_gained 0.12
fprA 3474304 p.Val100Leu missense_variant 0.12
Rv3236c 3613123 c.-7T>G upstream_gene_variant 0.17
fbiA 3640402 c.-141C>A upstream_gene_variant 0.12
fbiB 3642206 p.Asp224Glu missense_variant 0.15
rpoA 3877987 p.Val174Ala missense_variant 0.13
rpoA 3878489 p.Pro7Thr missense_variant 0.12
clpC1 4038293 c.2412G>C synonymous_variant 0.11
clpC1 4038668 c.2037G>T synonymous_variant 0.17
clpC1 4038752 p.Gln651His missense_variant 0.12
clpC1 4039730 c.975C>A synonymous_variant 0.12
clpC1 4039888 p.Leu273Ile missense_variant 0.17
panD 4044336 c.-55G>T upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244348 p.Trp372Cys missense_variant 0.12
embA 4244730 c.1499delT frameshift_variant 0.14
embA 4245770 p.Asn846Lys missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.48
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.46
embB 4246563 p.Leu17Trp missense_variant 0.37
embB 4246567 c.54G>T synonymous_variant 0.41
embB 4247024 p.Pro171Ala missense_variant 0.2
embB 4248212 c.1702delC frameshift_variant 0.17
embB 4249396 c.2883C>T synonymous_variant 0.14
aftB 4267067 c.1770C>T synonymous_variant 0.12
ethR 4328104 p.Ser186Thr missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0