TB-Profiler result

Run: ERR2229315
Summary

Run ID: ERR2229315

Sample name:

Date: 31-03-2023 16:59:44

Number of reads: 799931

Percentage reads mapped: 98.76

Strain: lineage4

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
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 576108 p.Ala254Gly missense_variant 0.4
ccsA 620669 p.Gly260Val missense_variant 0.11
rpoC 763673 p.Thr102Ala missense_variant 0.11
rpoC 764157 p.Lys263Arg missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776003 c.2478C>T synonymous_variant 0.17
mmpL5 776008 p.His825Asp missense_variant 0.17
mmpL5 776009 c.2472A>G synonymous_variant 0.17
mmpL5 776018 c.2463G>C synonymous_variant 0.18
mmpL5 776021 c.2460G>C synonymous_variant 0.18
mmpL5 777149 p.Asn444Lys missense_variant 0.27
mmpL5 777157 c.1324C>A synonymous_variant 0.27
mmpL5 777164 c.1317C>T synonymous_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406403 p.Val313Asp missense_variant 0.33
embR 1417429 c.-82G>A upstream_gene_variant 0.11
embR 1417497 c.-150C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473718 n.61G>T non_coding_transcript_exon_variant 0.15
rrl 1473732 n.77delC non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474281 n.624A>T non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.48
inhA 1674355 p.Asp52His missense_variant 0.25
rpsA 1834482 p.Glu314Gly missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918255 p.Ala106Ser missense_variant 0.12
ndh 2102875 c.168C>T synonymous_variant 0.33
katG 2154064 p.Gly683Val missense_variant 0.15
katG 2154462 c.1650C>T synonymous_variant 0.18
katG 2155344 c.768C>G synonymous_variant 0.2
PPE35 2167832 c.2781G>A synonymous_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168778 c.1834delA frameshift_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.2
PPE35 2169293 c.1320T>C synonymous_variant 0.14
PPE35 2169602 c.1011C>A synonymous_variant 0.23
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.61
PPE35 2170392 p.Gly74Ala missense_variant 0.19
PPE35 2170528 p.Ser29Thr missense_variant 0.15
PPE35 2170532 c.81G>C synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518888 c.774C>A synonymous_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.4
kasA 2519143 c.1029G>C synonymous_variant 0.4
eis 2715398 c.-66T>A upstream_gene_variant 0.14
pepQ 2860030 p.Ser130* stop_gained 0.13
pepQ 2860469 c.-51C>A upstream_gene_variant 0.14
Rv2752c 3064709 c.1483C>A synonymous_variant 0.5
Rv2752c 3064990 p.Arg401Gln missense_variant 0.15
Rv2752c 3065659 p.Pro178Leu missense_variant 0.11
Rv2752c 3066370 c.-179G>T upstream_gene_variant 0.12
thyX 3068065 c.-120G>C upstream_gene_variant 0.12
thyX 3068071 c.-126C>T upstream_gene_variant 0.12
thyX 3068083 c.-138T>C upstream_gene_variant 0.13
thyX 3068091 c.-146T>G upstream_gene_variant 0.13
thyA 3074177 c.295C>A synonymous_variant 0.12
ald 3087709 p.Cys297Phe missense_variant 0.17
fbiD 3339321 c.204G>C synonymous_variant 0.18
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.15
Rv3236c 3612165 p.Val318Met missense_variant 0.22
Rv3236c 3612698 p.Leu140Gln missense_variant 0.4
fbiA 3640803 p.His87Gln missense_variant 0.12
fbiB 3641624 c.90C>T synonymous_variant 0.2
alr 3840688 c.732delC frameshift_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.3
rpoA 3877815 c.693C>T synonymous_variant 0.25
clpC1 4038267 p.Gly813Val missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4039730 c.975C>G synonymous_variant 0.36
panD 4044372 c.-91T>C upstream_gene_variant 0.2
embC 4239878 c.20delC frameshift_variant 0.12
embC 4241118 c.1257_1258insGGCAGC conservative_inframe_insertion 0.15
embC 4241578 c.1716G>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243157 c.-76G>T upstream_gene_variant 0.15
embA 4243417 p.Leu62Pro missense_variant 0.5
embA 4244136 p.Ala302Ser missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.42
embB 4246555 c.42G>C synonymous_variant 0.47
embB 4246556 p.Ala15Pro missense_variant 0.47
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4246584 p.Arg24Pro missense_variant 0.18
embB 4247028 p.Leu172Arg missense_variant 0.38
embB 4248781 p.Glu756Asp missense_variant 0.18
aftB 4267145 c.1692G>C synonymous_variant 0.11
aftB 4267954 p.Ala295Pro missense_variant 0.18
aftB 4268501 c.336C>G synonymous_variant 0.12
ethA 4327085 p.Thr130Asn missense_variant 0.22
ethR 4327456 c.-93G>A upstream_gene_variant 0.14
ethA 4328244 c.-771G>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.15