TB-Profiler result

Run: ERR2229400
Summary

Run ID: ERR2229400

Sample name:

Date: 31-03-2023 17:09:30

Number of reads: 894983

Percentage reads mapped: 99.02

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 490667 c.-116C>A upstream_gene_variant 0.14
mshA 575517 p.Leu57Arg missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.39
rpoB 761152 p.Leu449Gln missense_variant 0.11
rpoB 761410 p.Val535Glu missense_variant 0.13
rpoC 764137 p.Met256Ile missense_variant 0.2
rpoC 765638 p.Glu757Gln missense_variant 0.12
rpoC 766505 p.Ile1046Phe missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775872 p.Ile870Asn missense_variant 0.25
mmpL5 776080 p.Ala801Ser missense_variant 0.17
mmpL5 776081 c.2400G>A synonymous_variant 0.15
mmpL5 776463 p.Ser673Leu missense_variant 0.15
mmpL5 777164 c.1317C>T synonymous_variant 0.11
mmpL5 777842 c.639C>A synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801244 p.Arg146Cys missense_variant 0.12
rplC 801287 p.Val160Glu missense_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417399 c.-52G>A upstream_gene_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
rrl 1476295 n.2638C>A non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
inhA 1674805 p.Ile202Phe missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102347 c.696G>T synonymous_variant 0.17
katG 2156435 c.-325delC upstream_gene_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.3
PPE35 2167967 c.2646A>C synonymous_variant 0.3
PPE35 2168728 p.Gly629Arg missense_variant 0.98
PPE35 2169231 p.Thr461Met missense_variant 0.17
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.58
Rv1979c 2222444 p.Ala241Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289971 c.-730T>C upstream_gene_variant 0.11
folC 2746541 p.Ala353Glu missense_variant 0.25
folC 2747306 p.Ser98Asn missense_variant 0.17
ribD 2987076 p.Val80Ile missense_variant 0.17
Rv2752c 3064864 p.Pro443Arg missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.16
clpC1 4039344 p.Glu454Gly missense_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.11
clpC1 4040408 c.297C>A synonymous_variant 0.12
embC 4242113 p.Leu751Met missense_variant 0.12
embA 4242625 c.-608T>C upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243216 c.-17G>C upstream_gene_variant 0.12
embA 4244951 c.1721delT frameshift_variant 0.13
embA 4245511 c.2281delG frameshift_variant 0.13
embB 4246567 c.54G>T synonymous_variant 0.22
embB 4246584 p.Arg24Pro missense_variant 0.25
embB 4249661 p.Ala1050Thr missense_variant 0.33
aftB 4267899 p.Ala313Asp missense_variant 0.17
ubiA 4269149 p.Val229Met missense_variant 0.13
ubiA 4269152 p.Ala228Pro missense_variant 0.14
ubiA 4269356 p.Arg160Cys missense_variant 0.13
ethR 4327453 c.-96A>G upstream_gene_variant 0.11
ethR 4327819 p.Ala91Thr missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407605 p.Ala200Ser missense_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0