TB-Profiler result

Run: SRR3732622
Summary

Run ID: SRR3732622

Sample name:

Date: 04-04-2023 05:36:43

Number of reads: 1287462

Percentage reads mapped: 99.64

Strain: lineage4.3.3

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrB 5702 p.Pro155Ser missense_variant 0.14
gyrA 6754 c.-548C>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7968 p.Val223Ile missense_variant 0.22
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8446 p.Arg382His missense_variant 0.17
gyrA 8940 p.Ala547Ser missense_variant 0.15
gyrA 9245 c.1944C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9811 c.2511delC frameshift_variant 0.2
fgd1 490832 p.Pro17Gln missense_variant 0.15
fgd1 490862 p.Ala27Val missense_variant 0.15
fgd1 490984 p.Leu68Met missense_variant 0.18
mshA 575600 p.Glu85* stop_gained 0.18
mshA 575626 c.279C>T synonymous_variant 0.14
mshA 575652 p.Arg102Leu missense_variant 0.14
mshA 576244 c.897C>T synonymous_variant 1.0
mshA 576361 c.1014C>A synonymous_variant 0.12
rpoB 759833 c.27A>G synonymous_variant 0.22
rpoB 760488 p.Val228Phe missense_variant 0.2
rpoB 760516 p.Trp237Leu missense_variant 0.15
rpoB 760599 p.Asp265Tyr missense_variant 0.15
rpoB 760943 c.1137C>A synonymous_variant 0.12
rpoB 761702 c.1896C>A synonymous_variant 0.17
rpoB 763097 p.Tyr1097* stop_gained 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765570 p.Ala734Val missense_variant 0.2
rpoC 766468 p.Glu1033Asp missense_variant 0.11
rpoC 766481 c.3112C>A synonymous_variant 0.12
rpoC 766558 p.Lys1063Asn missense_variant 0.17
rpoC 766687 p.Glu1106Asp missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777711 p.Gly257Val missense_variant 0.12
rpsL 781387 c.-173G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781737 p.Gln60* stop_gained 0.17
rplC 800742 c.-67G>A upstream_gene_variant 0.2
fbiC 1304628 c.1698G>T synonymous_variant 0.14
fbiC 1305389 p.Ala820Val missense_variant 0.15
Rv1258c 1406576 p.Gln255His missense_variant 0.22
Rv1258c 1407044 c.297C>T synonymous_variant 0.13
embR 1416372 p.Ser326Gly missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673301 c.-139G>A upstream_gene_variant 0.13
inhA 1674197 c.-5C>A upstream_gene_variant 0.25
rpsA 1833425 c.-117C>T upstream_gene_variant 0.2
rpsA 1833507 c.-35C>A upstream_gene_variant 0.2
rpsA 1834444 c.903C>T synonymous_variant 0.15
rpsA 1834958 p.Leu473Met missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918549 p.Arg204Ser missense_variant 0.12
ndh 2103192 c.-150G>T upstream_gene_variant 0.13
katG 2154037 p.Ser692Ile missense_variant 0.18
katG 2154183 c.1929G>T synonymous_variant 0.15
katG 2154449 p.Ala555Ser missense_variant 0.18
katG 2154473 p.Gly547Cys missense_variant 0.25
katG 2154515 p.Pro533Ser missense_variant 0.29
katG 2154610 p.Pro501Arg missense_variant 0.12
katG 2154762 c.1350C>T synonymous_variant 0.12
katG 2156436 c.-325C>A upstream_gene_variant 0.14
katG 2156476 c.-365G>A upstream_gene_variant 0.14
katG 2156552 c.-441C>G upstream_gene_variant 0.1
PPE35 2169041 c.1572G>A synonymous_variant 0.25
PPE35 2169053 c.1560T>C synonymous_variant 0.2
PPE35 2169893 c.720C>A synonymous_variant 0.17
Rv1979c 2221747 p.Arg473Gln missense_variant 0.15
Rv1979c 2222424 c.741G>T synonymous_variant 0.12
Rv1979c 2223138 c.27T>C synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289447 c.-206G>T upstream_gene_variant 0.13
pncA 2289692 c.-451C>T upstream_gene_variant 0.14
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519322 p.Gly403Glu missense_variant 0.14
folC 2746386 p.His405Asn missense_variant 0.15
folC 2747236 c.363G>T synonymous_variant 0.12
folC 2747790 c.-192G>T upstream_gene_variant 0.2
pepQ 2859509 p.Glu304* stop_gained 0.29
pepQ 2859521 c.898C>T synonymous_variant 0.18
pepQ 2859619 p.Gly267Val missense_variant 0.14
Rv2752c 3064623 c.1569C>A synonymous_variant 0.13
thyX 3067996 c.-51G>T upstream_gene_variant 0.14
thyX 3068115 c.-170C>T upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087819 c.1000C>A synonymous_variant 0.12
fprA 3473893 c.-114G>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474024 c.18C>T synonymous_variant 0.18
fprA 3474165 c.159C>G synonymous_variant 0.14
whiB7 3568441 p.Lys80Arg missense_variant 0.14
Rv3236c 3612351 p.Ala256Ser missense_variant 0.4
fbiA 3641153 p.Ala204Asp missense_variant 0.12
fbiA 3641180 p.Pro213Gln missense_variant 0.13
fbiB 3641683 p.Ser50Ile missense_variant 0.18
fbiB 3642505 p.Asp324Gly missense_variant 0.14
alr 3841510 c.-90A>G upstream_gene_variant 0.15
rpoA 3877932 c.576G>T synonymous_variant 0.22
rpoA 3878305 p.Gly68Val missense_variant 0.12
rpoA 3878454 c.54A>T synonymous_variant 0.33
clpC1 4038237 p.Thr823Ile missense_variant 0.14
clpC1 4038242 c.2463C>T synonymous_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038493 p.Val738Phe missense_variant 0.17
clpC1 4038534 p.Arg724Leu missense_variant 0.17
clpC1 4039546 p.Asp387Tyr missense_variant 0.25
clpC1 4039670 c.1035G>T synonymous_variant 0.22
clpC1 4039775 c.930G>T synonymous_variant 0.14
clpC1 4039998 p.Gly236Val missense_variant 0.13
panD 4044232 p.Cys17Phe missense_variant 0.18
embC 4241563 c.1701C>A synonymous_variant 0.12
embC 4242173 p.Ala771Pro missense_variant 0.29
embC 4242317 p.Glu819* stop_gained 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243056 p.Pro1065His missense_variant 0.17
embA 4243471 p.Ala80Val missense_variant 0.13
embA 4243709 c.477C>A synonymous_variant 0.14
embA 4244486 c.1254C>G synonymous_variant 0.15
embA 4244574 p.Ala448Ser missense_variant 0.17
embA 4245354 p.Ala708Ser missense_variant 0.17
embB 4248222 p.Pro570Gln missense_variant 0.17
embB 4249035 p.Arg841Leu missense_variant 0.12
aftB 4267928 c.909G>A synonymous_variant 0.18
aftB 4268561 c.276G>T synonymous_variant 0.22
aftB 4268595 c.241delT frameshift_variant 0.25
aftB 4268732 c.105G>C synonymous_variant 1.0
ubiA 4268939 p.Val299Ile missense_variant 0.17
aftB 4269228 c.-392C>A upstream_gene_variant 0.12
aftB 4269357 c.-521C>A upstream_gene_variant 0.22
ethR 4326592 c.-957G>A upstream_gene_variant 0.13
ethR 4326850 c.-699T>C upstream_gene_variant 0.18
ethR 4327219 c.-330G>C upstream_gene_variant 0.2
ethR 4327646 p.Ala33Asp missense_variant 0.17
ethR 4328077 p.Leu177Met missense_variant 0.12
whiB6 4338467 p.Val19Leu missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408103 p.Gly34Trp missense_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0