TB-Profiler result

Run: ERR7801203

Summary

Run ID: ERR7801203

Sample name:

Date: 02-04-2023 05:58:42

Number of reads: 734172

Percentage reads mapped: 99.25

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.96
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.97
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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrB 7265 c.2026T>C stop_lost&splice_region_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491031 c.249C>A synonymous_variant 0.17
fgd1 491279 p.Pro166His missense_variant 0.2
fgd1 491320 p.Ala180Ser missense_variant 0.22
fgd1 491328 c.546C>A synonymous_variant 0.25
ccsA 619828 c.-63G>T upstream_gene_variant 0.18
ccsA 619849 c.-42G>T upstream_gene_variant 0.17
ccsA 620127 c.237C>A synonymous_variant 0.2
ccsA 620632 p.Ala248Ser missense_variant 0.14
rpoB 759746 c.-61C>A upstream_gene_variant 0.15
rpoB 759763 c.-44C>A upstream_gene_variant 0.23
rpoB 761328 p.Thr508Pro missense_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765023 p.Gln552* stop_gained 0.19
rpoC 765740 c.2372delA frameshift_variant 0.1
mmpL5 775631 p.Gln950His missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777427 p.Thr352Ala missense_variant 0.11
mmpL5 777734 p.Phe249Leu missense_variant 0.2
mmpL5 778329 p.Pro51Gln missense_variant 0.17
mmpR5 779374 p.Pro129Thr missense_variant 0.15
mmpS5 779572 c.-667G>T upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303443 p.Leu171Phe missense_variant 0.15
fbiC 1303642 p.Pro238Thr missense_variant 0.21
fbiC 1303705 p.Leu259Met missense_variant 0.17
fbiC 1304132 p.Ala401Glu missense_variant 0.17
fbiC 1304236 p.Gln436Lys missense_variant 0.17
fbiC 1304348 p.Trp473Leu missense_variant 0.17
Rv1258c 1407191 c.150G>T synonymous_variant 0.19
Rv1258c 1407537 c.-197G>A upstream_gene_variant 0.29
embR 1416452 p.Arg299Leu missense_variant 0.22
atpE 1460852 c.-193C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472547 n.702G>T non_coding_transcript_exon_variant 0.15
rrl 1473717 n.60G>T non_coding_transcript_exon_variant 0.17
rrl 1475517 n.1860C>A non_coding_transcript_exon_variant 0.18
inhA 1674622 p.Gly141Arg missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154822 c.1290G>T synonymous_variant 0.19
katG 2154865 p.Ile416Ser missense_variant 0.29
katG 2155230 p.Glu294Asp missense_variant 0.17
katG 2156434 c.-323G>T upstream_gene_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289476 c.-235G>C upstream_gene_variant 0.11
kasA 2519087 p.Ala325Ser missense_variant 0.17
folC 2746216 p.Phe461Leu missense_variant 0.18
Rv2752c 3066998 c.-807G>C upstream_gene_variant 0.11
thyX 3067418 c.528C>A synonymous_variant 0.19
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073986 p.Gln162His missense_variant 0.15
thyA 3074575 c.-104G>T upstream_gene_variant 0.18
thyA 3074630 c.-159C>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339337 p.Gly74Trp missense_variant 0.22
fbiD 3339463 p.Asp116Tyr missense_variant 0.2
Rv3083 3449070 c.567G>T synonymous_variant 0.29
Rv3083 3449337 c.834C>A synonymous_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474079 p.Ala25Ser missense_variant 0.14
fprA 3474236 p.Arg77His missense_variant 0.17
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612789 p.Leu110Phe missense_variant 0.15
fbiA 3640774 p.Gly78Cys missense_variant 0.21
fbiB 3641304 c.-231C>A upstream_gene_variant 0.15
fbiB 3642004 p.Arg157His missense_variant 0.22
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3841405 p.Glu6* stop_gained 0.18
rpoA 3878483 p.Leu9Met missense_variant 0.15
ddn 3986860 p.Pro6Gln missense_variant 0.19
ddn 3986948 p.Glu35Asp missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038842 c.1863G>A synonymous_variant 0.33
embC 4242368 p.Arg836Ser missense_variant 0.18
embC 4242456 p.Arg865Leu missense_variant 0.18
embC 4242524 p.Ala888Ser missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243968 p.Val246Ile missense_variant 0.13
embA 4244220 p.Leu330Val missense_variant 0.12
embA 4244489 c.1257G>T synonymous_variant 0.18
embB 4245653 c.-861C>T upstream_gene_variant 0.18
embA 4246298 p.Gln1022His missense_variant 0.12
embB 4246980 p.Gly156Val missense_variant 0.15
embB 4247207 p.Ala232Pro missense_variant 1.0
embB 4248505 c.1995delG frameshift_variant 0.11
aftB 4267710 p.Ser376Ile missense_variant 0.15
aftB 4268680 p.Glu53Lys missense_variant 0.18
ubiA 4268944 c.889delG frameshift_variant 0.11
ubiA 4269864 c.-32delG upstream_gene_variant 0.2
ethR 4327618 p.Asp24Tyr missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
PPE35 2158030 c.-22_*9618del transcript_ablation 1.0