TB-Profiler result

Run: ERR4817024
Summary

Run ID: ERR4817024

Sample name:

Date: 01-04-2023 14:45:41

Number of reads: 897415

Percentage reads mapped: 99.59

Strain: lineage4.6.5

Drug-resistance: HR-TB

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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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.5 Euro-American T;LAM None 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
tlyA 1918647 p.Asn236Lys missense_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrB 5489 p.Ile84Val missense_variant 1.0
gyrB 5813 p.Arg192Ser missense_variant 0.13
gyrB 7031 p.Gly598Trp missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8033 p.Tyr244* stop_gained 0.25
gyrA 8300 c.999G>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 0.9
fgd1 491395 p.Glu205Gln missense_variant 0.12
mshA 575521 c.174A>C synonymous_variant 0.12
mshA 575527 c.180G>C synonymous_variant 0.12
mshA 575536 c.189T>C synonymous_variant 0.15
mshA 575542 c.195C>G synonymous_variant 0.15
mshA 575561 p.Met72Val missense_variant 0.12
mshA 575569 c.222A>G synonymous_variant 0.15
mshA 575571 p.Ser75Thr missense_variant 0.17
mshA 575576 c.229C>T synonymous_variant 0.17
mshA 575587 c.240C>G synonymous_variant 0.14
mshA 575590 c.243T>G synonymous_variant 0.14
mshA 575617 c.270C>G synonymous_variant 0.15
mshA 576369 p.Arg341Leu missense_variant 0.14
ccsA 620216 p.Asn109Ser missense_variant 0.11
rpoB 759715 c.-92G>A upstream_gene_variant 0.17
rpoB 760082 c.276C>T synonymous_variant 0.1
rpoB 760106 c.300G>T synonymous_variant 0.12
rpoB 760724 c.918T>C synonymous_variant 0.11
rpoB 760730 c.924T>C synonymous_variant 0.1
rpoB 760751 c.945G>C synonymous_variant 0.13
rpoB 761717 c.1911C>G synonymous_variant 0.2
rpoB 761959 p.Met718Lys missense_variant 0.11
rpoB 762199 p.Gly798Ala missense_variant 0.11
rpoB 762429 p.Asp875Tyr missense_variant 0.14
rpoB 762455 p.His883Gln missense_variant 0.14
rpoC 764672 p.Gln435* stop_gained 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777974 c.507C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304635 p.Gln569Lys missense_variant 0.12
fbiC 1304932 p.Ala668Ser missense_variant 0.11
atpE 1461008 c.-37G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673970 c.-232C>T upstream_gene_variant 0.12
inhA 1674545 p.Asp115Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918220 p.Gly94Val missense_variant 0.12
ndh 2102943 p.Lys34Glu missense_variant 0.11
PPE35 2170371 p.Thr81Val missense_variant 0.13
PPE35 2170469 c.144G>T synonymous_variant 0.17
Rv1979c 2222166 c.999C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.12
kasA 2518879 c.765A>G synonymous_variant 0.12
kasA 2518882 c.768C>A synonymous_variant 0.12
kasA 2518896 c.783_784delGT frameshift_variant 0.12
kasA 2519169 p.Ala352Glu missense_variant 0.17
kasA 2519244 p.Asp377Gly missense_variant 0.29
eis 2715038 p.Ala99Ser missense_variant 0.11
folC 2746362 p.Asp413Tyr missense_variant 0.13
folC 2746934 p.Arg222Pro missense_variant 0.15
folC 2746995 p.Val202Ile missense_variant 1.0
ribD 2987146 p.Arg103His missense_variant 0.12
thyX 3067714 p.Val78Met missense_variant 0.12
thyA 3074028 c.444G>C synonymous_variant 0.15
Rv3083 3449868 c.1365C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612537 p.Gly194Arg missense_variant 0.13
fbiA 3640346 c.-196delA upstream_gene_variant 1.0
fbiA 3640954 p.Pro138Ala missense_variant 0.14
fbiB 3640965 c.-570C>G upstream_gene_variant 0.13
fbiB 3640974 c.-561T>C upstream_gene_variant 0.13
rpoA 3878163 c.345C>T synonymous_variant 0.13
clpC1 4038332 c.2373C>T synonymous_variant 1.0
panD 4044088 p.Gly65Asp missense_variant 0.11
embC 4242588 p.Gly909Glu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245071 c.1839G>A synonymous_variant 0.13
embB 4248894 p.Pro794Gln missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0