TB-Profiler result

Run: SRR21277762
Summary

Run ID: SRR21277762

Sample name:

Date: 04-04-2023 01:39:32

Number of reads: 9512893

Percentage reads mapped: 99.21

Strain: lineage4.4.2

Drug-resistance: Other

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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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
embR 1416474 p.Leu292Met missense_variant 0.12 ethambutol
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490684 c.-99G>A upstream_gene_variant 0.11
fgd1 491305 p.Ala175Thr missense_variant 0.12
fgd1 491338 p.Gly186Cys missense_variant 0.17
mshA 575267 c.-81G>T upstream_gene_variant 0.12
mshA 575270 c.-78G>A upstream_gene_variant 0.11
mshA 575286 c.-62G>T upstream_gene_variant 0.15
mshA 575406 p.Arg20His missense_variant 0.18
mshA 576755 p.Arg470Ser missense_variant 0.11
mshA 576762 p.Trp472* stop_gained 0.12
ccsA 620224 p.Glu112* stop_gained 0.13
rpoB 761657 c.1851C>A synonymous_variant 0.11
rpoC 763158 c.-212C>T upstream_gene_variant 0.38
rpoC 765280 c.1911G>A synonymous_variant 0.2
rpoC 765314 p.Glu649* stop_gained 0.13
rpoC 766954 c.3585C>A synonymous_variant 0.12
rpoC 766990 c.3621G>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 777272 c.1209C>T synonymous_variant 0.11
mmpL5 779355 c.-875C>A upstream_gene_variant 0.12
mmpL5 779364 c.-884C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303133 p.Ala68Val missense_variant 0.19
Rv1258c 1406165 c.1176G>T synonymous_variant 0.13
Rv1258c 1407515 c.-175G>T upstream_gene_variant 0.17
embR 1416456 p.Gly298Cys missense_variant 0.13
embR 1416959 p.Arg130Leu missense_variant 0.14
embR 1416978 p.His124Asn missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917953 p.Ala5Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170107 p.Ala169Asp missense_variant 0.13
PPE35 2170342 p.Gln91* stop_gained 0.15
PPE35 2170418 p.Met65Ile missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715545 c.-213C>T upstream_gene_variant 0.11
folC 2746565 p.Ala345Val missense_variant 0.16
folC 2746663 p.Phe312Leu missense_variant 0.12
folC 2747119 p.Phe160Leu missense_variant 0.11
pepQ 2859579 c.840G>T synonymous_variant 0.13
pepQ 2859584 p.Gln279* stop_gained 0.14
pepQ 2859615 c.804C>A synonymous_variant 0.11
pepQ 2859942 c.477C>A synonymous_variant 0.4
pepQ 2859965 p.Ala152Thr missense_variant 0.14
pepQ 2860076 p.Glu115* stop_gained 0.11
pepQ 2860133 p.Gly96Cys missense_variant 0.18
ribD 2987308 p.Ala157Gly missense_variant 0.12
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
Rv2752c 3066302 c.-111C>A upstream_gene_variant 0.11
Rv2752c 3067154 c.-963G>T upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087275 c.456C>A synonymous_variant 0.12
ald 3087335 c.516G>T synonymous_variant 0.22
fbiD 3339034 c.-84G>T upstream_gene_variant 0.11
fbiD 3339052 c.-66G>T upstream_gene_variant 0.11
Rv3083 3448348 c.-156G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475298 p.Arg431Gln missense_variant 0.15
Rv3236c 3612177 c.940C>A synonymous_variant 0.12
fbiA 3641342 p.Ser267Tyr missense_variant 0.13
fbiB 3641609 c.75C>A synonymous_variant 0.18
fbiB 3641641 p.Ala36Val missense_variant 0.15
fbiB 3642477 p.Asp315Asn missense_variant 1.0
alr 3841201 p.Ala74Thr missense_variant 0.11
alr 3841612 c.-193_-192insC upstream_gene_variant 0.21
rpoA 3878605 c.-98G>T upstream_gene_variant 0.11
rpoA 3878608 c.-101C>A upstream_gene_variant 0.11
ddn 3986649 c.-195G>T upstream_gene_variant 0.13
clpC1 4038181 p.Gly842Cys missense_variant 0.13
clpC1 4038186 p.Ala840Val missense_variant 0.14
clpC1 4038194 c.2511G>A synonymous_variant 1.0
clpC1 4039873 p.Thr278Ser missense_variant 1.0
embC 4240411 c.549G>A synonymous_variant 0.17
embC 4240582 c.720C>A synonymous_variant 0.13
embC 4241002 c.1140G>A synonymous_variant 0.15
embC 4241680 c.1818C>A synonymous_variant 0.12
embC 4242368 p.Arg836Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243458 p.Cys76Ser missense_variant 0.12
embA 4243615 p.Arg128Leu missense_variant 0.2
embA 4243622 c.390G>T synonymous_variant 0.12
embA 4244305 p.Arg358Leu missense_variant 0.5
embA 4244310 p.Ala360Ser missense_variant 0.18
embA 4244603 c.1371G>T synonymous_variant 0.24
embA 4244606 c.1374G>T synonymous_variant 0.11
embA 4244923 p.Thr564Met missense_variant 0.11
embA 4245447 p.Val739Met missense_variant 0.12
embB 4246508 c.-6G>A upstream_gene_variant 1.0
embB 4247012 p.Pro167Thr missense_variant 0.12
embB 4247249 p.Gly246Arg missense_variant 1.0
embB 4247298 p.Pro262Leu missense_variant 0.11
embB 4247622 p.Leu370Gln missense_variant 0.12
embB 4247624 p.Pro371Thr missense_variant 0.25
embB 4247644 c.1131G>T synonymous_variant 0.29
embB 4247660 p.Ala383Ser missense_variant 0.14
embB 4247674 c.1161G>T synonymous_variant 0.11
embB 4247921 p.His470Tyr missense_variant 0.13
embB 4248591 p.Ala693Asp missense_variant 0.18
embB 4248597 p.Glu695Val missense_variant 0.15
embB 4249193 p.Pro894Thr missense_variant 0.1
embB 4249366 p.Glu951Asp missense_variant 0.12
aftB 4267904 c.933G>T synonymous_variant 0.15
aftB 4267974 p.Ser288* stop_gained 0.11
aftB 4268476 p.Gly121Trp missense_variant 0.1
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ubiA 4269707 p.Gly43Cys missense_variant 0.13
ethR 4327604 p.Arg19Leu missense_variant 0.15
whiB6 4338315 c.207C>A synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0