TB-Profiler result

Run: ERR2229628

Summary

Run ID: ERR2229628

Sample name:

Date: 31-03-2023 17:22:39

Number of reads: 1005060

Percentage reads mapped: 99.08

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 491518 p.Thr246Ala missense_variant 0.12
fgd1 491529 p.Trp249* stop_gained 0.13
mshA 575630 p.Ser95Pro missense_variant 0.25
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576747 p.Gly467Asp missense_variant 0.12
ccsA 620832 c.942C>T synonymous_variant 0.12
rpoB 760573 c.769delG frameshift_variant 0.13
rpoB 760794 p.Glu330Lys missense_variant 0.29
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 763216 p.Ala1137Glu missense_variant 0.12
rpoC 765496 c.2127C>A synonymous_variant 0.14
rpoC 766146 p.Gly926Ala missense_variant 0.11
rpoC 766787 p.Glu1140Lys missense_variant 0.15
rpoC 766796 p.Arg1143Ser missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.12
mmpL5 776021 c.2460G>C synonymous_variant 0.12
mmpL5 777164 c.1317C>T synonymous_variant 0.12
mmpL5 777753 c.727delA frameshift_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801000 c.192G>A synonymous_variant 0.2
rplC 801110 p.Leu101Ser missense_variant 0.18
fbiC 1302942 c.12T>C synonymous_variant 0.14
fbiC 1303493 p.Leu188Ser missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303941 c.1011G>T synonymous_variant 0.5
fbiC 1304335 p.Ala469Ser missense_variant 0.13
Rv1258c 1406252 c.1089T>A synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474026 n.369C>A non_coding_transcript_exon_variant 0.12
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.11
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.18
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
inhA 1674586 p.Ser129Pro missense_variant 0.2
inhA 1674600 c.399G>C synonymous_variant 0.2
rpsA 1834468 c.927A>T synonymous_variant 0.18
rpsA 1834806 p.Glu422Gly missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102663 p.Gly127Asp missense_variant 0.17
katG 2154863 p.His417Tyr missense_variant 0.14
PPE35 2167973 c.2640A>G synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.16
PPE35 2169272 c.1341C>G synonymous_variant 0.16
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169748 p.Ile289Phe missense_variant 0.12
PPE35 2169749 c.864A>C synonymous_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.42
PPE35 2170053 p.Thr187Ser missense_variant 0.39
Rv1979c 2223073 p.Gly31Asp missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518045 c.-70G>A upstream_gene_variant 0.13
kasA 2519057 p.Thr315Ser missense_variant 0.14
kasA 2519062 c.948T>G synonymous_variant 0.14
kasA 2519065 c.951C>A synonymous_variant 0.14
kasA 2519066 c.956_982delACGCCGCGGAGGCCAACGCCATCCGCG disruptive_inframe_deletion 0.13
kasA 2519140 c.1026G>C synonymous_variant 0.18
kasA 2519143 c.1029G>C synonymous_variant 0.18
kasA 2519283 p.Arg390His missense_variant 0.13
eis 2714653 p.Arg227Pro missense_variant 0.22
eis 2714667 c.666G>A synonymous_variant 0.18
eis 2714763 c.570G>A synonymous_variant 0.25
folC 2746587 c.1012C>A synonymous_variant 0.2
folC 2747175 p.Ala142Ser missense_variant 0.14
ribD 2986970 p.Asn44Lys missense_variant 0.2
Rv2752c 3064771 p.Ala474Glu missense_variant 0.22
Rv2752c 3065826 c.366A>T synonymous_variant 0.11
Rv2752c 3065985 c.207C>T synonymous_variant 0.12
thyX 3067442 c.504C>A synonymous_variant 0.13
thyX 3068031 c.-86A>G upstream_gene_variant 0.11
fbiD 3339270 c.153G>T synonymous_variant 0.15
fbiD 3339589 p.Leu158Val missense_variant 0.14
fbiD 3339734 p.Ala206Gly missense_variant 0.18
fprA 3474110 p.Ala35Asp missense_variant 0.12
Rv3236c 3612076 c.1041G>T synonymous_variant 0.12
Rv3236c 3613217 c.-101G>T upstream_gene_variant 0.13
fbiB 3642467 c.933T>C synonymous_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.17
alr 3841612 c.-193_-192insC upstream_gene_variant 0.16
rpoA 3877606 p.Leu301Pro missense_variant 0.12
clpC1 4038639 p.Asp689Gly missense_variant 0.13
clpC1 4039042 p.Ser555Thr missense_variant 0.15
clpC1 4039682 c.1023C>T synonymous_variant 0.13
clpC1 4039691 c.1014G>C synonymous_variant 0.11
clpC1 4039714 p.Tyr331His missense_variant 0.24
clpC1 4040464 c.240delT frameshift_variant 0.12
embC 4242234 p.Pro791His missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243607 c.375G>T synonymous_variant 0.15
embA 4244807 c.1575G>T synonymous_variant 0.18
embA 4246204 p.Arg991Gln missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.56
embB 4246555 c.42G>C synonymous_variant 0.62
embB 4246556 p.Ala15Pro missense_variant 0.54
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.44
embB 4246709 p.Ser66Gly missense_variant 0.17
embB 4249766 p.Arg1085Gly missense_variant 0.17
aftB 4268892 c.-56T>C upstream_gene_variant 0.17
aftB 4269590 c.-754C>A upstream_gene_variant 0.2
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0