TB-Profiler result

Run: ERR2228811
Summary

Run ID: ERR2228811

Sample name:

Date: 31-03-2023 16:22:03

Number of reads: 831683

Percentage reads mapped: 99.23

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
gyrA 8685 p.Ile462Val missense_variant 0.12
mshA 575895 p.Val183Ala missense_variant 0.12
mshA 576067 c.720C>A synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.45
mshA 576351 p.Asp335Gly missense_variant 0.17
rpoB 759695 c.-112G>A upstream_gene_variant 0.17
rpoC 764019 p.Asp217Ala missense_variant 0.11
rpoC 764962 c.1593G>A synonymous_variant 0.13
rpoC 765106 c.1737G>A synonymous_variant 0.13
rpoC 766392 p.Thr1008Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 c.2755C>T synonymous_variant 0.18
mmpL5 775727 c.2754C>G synonymous_variant 0.18
mmpL5 775736 c.2745C>G synonymous_variant 0.22
mmpL5 775741 c.2740C>T synonymous_variant 0.25
mmpL5 775747 p.Met912Leu missense_variant 0.18
mmpL5 775748 c.2733T>C synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777157 c.1324C>A synonymous_variant 0.15
mmpL5 777164 c.1317C>T synonymous_variant 0.15
mmpL5 777420 p.Gly354Val missense_variant 0.12
mmpL5 777867 p.Gln205Arg missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302951 c.21G>T synonymous_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406265 p.Ala359Asp missense_variant 0.12
Rv1258c 1406289 p.Val351Ala missense_variant 0.11
Rv1258c 1406866 p.Ala159Ser missense_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
inhA 1674504 c.303C>T synonymous_variant 0.15
rpsA 1833917 p.Val126Phe missense_variant 0.13
rpsA 1834309 c.768C>T synonymous_variant 0.22
rpsA 1834586 p.Ile349Phe missense_variant 0.33
rpsA 1834652 p.Glu371* stop_gained 0.2
rpsA 1834932 p.Leu464Pro missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102530 c.513G>T synonymous_variant 0.25
ndh 2102921 p.Lys41Thr missense_variant 0.29
ndh 2103212 c.-170A>T upstream_gene_variant 0.14
katG 2155182 c.930G>A synonymous_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.18
PPE35 2167967 c.2646A>C synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169281 c.1332T>G synonymous_variant 0.13
PPE35 2169287 c.1326T>C synonymous_variant 0.16
PPE35 2169884 c.729T>C synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2169910 p.Asn235Tyr missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.34
PPE35 2170053 p.Thr187Ser missense_variant 0.4
PPE35 2170147 p.Ser156Ala missense_variant 0.16
PPE35 2170454 c.159C>G synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289752 c.-511G>T upstream_gene_variant 0.17
kasA 2519128 c.1014G>C synonymous_variant 0.19
kasA 2519131 c.1017G>C synonymous_variant 0.19
kasA 2519140 c.1026G>C synonymous_variant 0.23
kasA 2519143 c.1029G>C synonymous_variant 0.24
kasA 2519268 p.Val385Ala missense_variant 0.17
eis 2714962 p.Gly124Asp missense_variant 0.25
eis 2715111 p.Glu74Asp missense_variant 0.12
eis 2715432 c.-100C>T upstream_gene_variant 0.18
eis 2715436 c.-104G>A upstream_gene_variant 0.18
eis 2715440 c.-108A>C upstream_gene_variant 0.2
eis 2715445 c.-113C>T upstream_gene_variant 0.22
eis 2715447 c.-115T>A upstream_gene_variant 0.22
eis 2715450 c.-118T>C upstream_gene_variant 0.22
eis 2715451 c.-119C>A upstream_gene_variant 0.22
eis 2715454 c.-122T>G upstream_gene_variant 0.25
eis 2715455 c.-123G>A upstream_gene_variant 0.22
eis 2715458 c.-126T>A upstream_gene_variant 0.22
eis 2715460 c.-128A>G upstream_gene_variant 0.22
eis 2715465 c.-133G>T upstream_gene_variant 0.22
eis 2715469 c.-137T>C upstream_gene_variant 0.22
eis 2715473 c.-141A>G upstream_gene_variant 0.25
folC 2747003 p.Ile199Asn missense_variant 0.13
folC 2747450 p.Ile50Thr missense_variant 0.29
ald 3087726 p.Ala303Thr missense_variant 0.18
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474662 p.Asp219Val missense_variant 0.12
whiB7 3568817 c.-138C>A upstream_gene_variant 0.14
Rv3236c 3612680 p.Arg146Gln missense_variant 0.14
alr 3840594 p.Thr276Ile missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.2
clpC1 4039645 p.His354Asp missense_variant 0.36
clpC1 4040144 c.561G>C synonymous_variant 0.18
embC 4241652 p.Ala597Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243743 p.Gly171Ser missense_variant 0.15
embA 4243908 p.Arg226Trp missense_variant 0.14
embB 4246846 p.Leu111Phe missense_variant 0.12
embB 4247426 p.Gly305Thr missense_variant 0.15
embB 4247602 c.1089G>A synonymous_variant 0.18
embB 4249654 c.3141C>T synonymous_variant 0.12
aftB 4267933 p.Ala302Pro missense_variant 0.15
aftB 4268731 p.Arg36Trp missense_variant 0.13
ubiA 4269110 p.Gly242Ser missense_variant 0.15
aftB 4269147 c.-311G>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0