TB-Profiler result

Run: SRR4035767

Summary

Run ID: SRR4035767

Sample name:

Date: 04-04-2023 07:17:09

Number of reads: 842286

Percentage reads mapped: 99.49

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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 1416660 p.Arg230Trp missense_variant 0.22 ethambutol
ethA 4326648 c.825dupG frameshift_variant 0.18 ethionamide, ethionamide
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 5602 c.363C>T synonymous_variant 0.18
gyrA 7292 c.-10C>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7784 p.Gln161His missense_variant 0.25
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8676 p.Glu459Lys missense_variant 0.17
gyrA 8693 p.Asp464Glu missense_variant 0.15
gyrA 8802 p.Ala501Thr missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9748 p.Ala816Val missense_variant 0.17
fgd1 491176 p.Leu132Met missense_variant 0.17
fgd1 491362 p.Cys194Ser missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575898 p.Lys184Met missense_variant 0.29
mshA 575917 c.570_571insA frameshift_variant 0.67
mshA 575926 c.579A>G synonymous_variant 0.67
mshA 575933 p.Pro196Ser missense_variant 0.4
ccsA 619692 c.-199T>C upstream_gene_variant 0.2
ccsA 619705 c.-186G>A upstream_gene_variant 0.18
ccsA 620364 c.476delA frameshift_variant 0.13
ccsA 620525 p.Leu212Pro missense_variant 0.22
rpoB 759973 p.Glu56Val missense_variant 0.15
rpoB 759977 p.Trp57Cys missense_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761024 c.1218C>T synonymous_variant 0.33
rpoB 762088 p.Glu761Val missense_variant 0.15
rpoB 762229 p.Leu808Pro missense_variant 0.18
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775945 p.Val846Ile missense_variant 0.13
mmpL5 776461 p.Ala674Thr missense_variant 0.13
mmpL5 777299 c.1182G>T synonymous_variant 0.18
mmpL5 777317 c.1164C>T synonymous_variant 0.2
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpS5 779486 c.-581C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303690 p.Pro254Ala missense_variant 0.12
fbiC 1304130 p.Gln400His missense_variant 0.22
fbiC 1305252 c.2322G>A synonymous_variant 0.17
Rv1258c 1406989 p.Pro118Ala missense_variant 0.12
embR 1417409 c.-62C>G upstream_gene_variant 0.15
embR 1417506 c.-159T>C upstream_gene_variant 0.17
embR 1417540 c.-193C>T upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472978 n.1133T>A non_coding_transcript_exon_variant 0.15
rrs 1473198 n.1353G>A non_coding_transcript_exon_variant 0.29
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.12
rrl 1476318 n.2661T>C non_coding_transcript_exon_variant 0.12
fabG1 1673436 c.-3delG upstream_gene_variant 0.12
fabG1 1674056 p.Ile206Asn missense_variant 0.2
inhA 1674383 p.Leu61His missense_variant 0.17
rpsA 1833570 p.Gln10Leu missense_variant 0.14
rpsA 1833605 p.Phe22Ile missense_variant 0.15
rpsA 1834965 p.Glu475Gly missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917996 c.57A>T synonymous_variant 0.22
tlyA 1918012 p.Glu25Lys missense_variant 0.25
tlyA 1918215 c.276G>A synonymous_variant 0.17
tlyA 1918556 p.Arg206Gln missense_variant 0.17
ndh 2101853 p.Leu397Pro missense_variant 0.17
ndh 2102280 p.Asn255Asp missense_variant 0.13
ndh 2102304 p.Ala247Thr missense_variant 0.18
ndh 2102757 p.Gly96Arg missense_variant 0.11
ndh 2103161 c.-119G>C upstream_gene_variant 0.15
katG 2155101 p.Tyr337* stop_gained 0.17
katG 2155986 c.126G>A synonymous_variant 0.17
katG 2156364 c.-253T>A upstream_gene_variant 0.18
PPE35 2167658 c.2955C>T synonymous_variant 0.18
PPE35 2167676 c.2937C>T synonymous_variant 0.18
PPE35 2167705 p.Leu970Met missense_variant 0.17
PPE35 2167713 p.Val967Asp missense_variant 0.13
PPE35 2168317 p.Thr766Ser missense_variant 0.17
Rv1979c 2222729 p.Gly146Arg missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288943 p.Thr100Ser missense_variant 0.12
pncA 2289548 c.-307C>A upstream_gene_variant 0.13
pncA 2289649 c.-408G>C upstream_gene_variant 0.12
pncA 2289655 c.-414G>C upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518415 p.Pro101Ser missense_variant 0.13
kasA 2518455 p.Thr114Ile missense_variant 0.14
ahpC 2726003 c.-190C>T upstream_gene_variant 0.13
ahpC 2726005 c.-188G>A upstream_gene_variant 0.13
ahpC 2726071 c.-122C>G upstream_gene_variant 0.12
ahpC 2726182 c.-11T>C upstream_gene_variant 0.14
ahpC 2726501 c.313delA frameshift_variant 0.12
pepQ 2860302 c.117C>T synonymous_variant 0.18
ribD 2986720 c.-119C>T upstream_gene_variant 0.13
ribD 2986734 c.-105G>A upstream_gene_variant 0.14
ribD 2987237 p.Phe133Leu missense_variant 0.17
ribD 2987595 c.760delC frameshift_variant 0.13
ribD 2987604 p.Val256Ile missense_variant 0.13
Rv2752c 3064856 p.Lys446Glu missense_variant 0.33
Rv2752c 3066358 c.-167G>A upstream_gene_variant 0.2
thyX 3067437 p.Ala170Gly missense_variant 0.2
thyA 3074441 p.Val11Met missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087136 c.322_324delTTG conservative_inframe_deletion 0.22
ald 3087924 p.Val369Leu missense_variant 0.13
Rv3083 3448455 c.-49T>A upstream_gene_variant 0.22
Rv3083 3448749 c.246G>A synonymous_variant 0.13
Rv3083 3449183 p.Ser227Phe missense_variant 0.12
Rv3083 3449223 p.Tyr240* stop_gained 0.12
Rv3083 3449236 p.Arg245Gly missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475061 p.Pro352His missense_variant 0.18
Rv3236c 3611973 p.Val382Ile missense_variant 0.18
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
fbiA 3641380 p.Cys280Ser missense_variant 0.13
fbiB 3641803 p.Asp90Gly missense_variant 0.12
fbiB 3642049 p.Val172Ala missense_variant 0.12
fbiB 3642261 p.Leu243Val missense_variant 0.14
alr 3841546 c.-126C>T upstream_gene_variant 0.14
rpoA 3877604 p.His302Tyr missense_variant 0.15
ddn 3987240 p.Tyr133His missense_variant 0.14
clpC1 4038749 c.1956C>T synonymous_variant 0.18
clpC1 4039958 c.747G>T synonymous_variant 0.18
panD 4043954 p.Ala110Pro missense_variant 0.13
panD 4044211 p.Gly24Asp missense_variant 0.15
panD 4044240 c.42G>A synonymous_variant 0.14
panD 4044369 c.-88A>T upstream_gene_variant 0.14
embC 4240134 p.Ala91Gly missense_variant 0.15
embC 4241824 c.1962T>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242768 p.Arg969Pro missense_variant 0.18
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243110 p.Ser1083Asn missense_variant 0.15
embA 4243117 c.-116G>A upstream_gene_variant 0.14
embA 4243250 c.18T>C synonymous_variant 0.12
embA 4243588 p.Arg119His missense_variant 0.22
embA 4243591 p.Asp120Val missense_variant 0.2
embA 4243719 p.Pro163Ser missense_variant 0.12
embA 4243952 c.720T>C synonymous_variant 0.12
embB 4246723 c.210G>A synonymous_variant 0.18
embB 4247522 p.Leu337Met missense_variant 0.22
embB 4249212 p.Leu900Pro missense_variant 0.11
embB 4249410 p.Pro966Leu missense_variant 0.14
embB 4249634 p.Asp1041Asn missense_variant 0.25
aftB 4266974 c.1863C>T synonymous_variant 0.15
aftB 4267602 p.Arg412His missense_variant 0.2
aftB 4268982 c.-146G>A upstream_gene_variant 0.22
ethA 4326064 c.1410C>T synonymous_variant 0.2
ethA 4326202 c.1272A>T synonymous_variant 0.18
ethA 4326710 p.Lys255Met missense_variant 0.18
ethR 4327084 c.-465G>C upstream_gene_variant 0.25
ethA 4327155 p.Ala107Thr missense_variant 0.2
ethA 4327665 c.-192G>A upstream_gene_variant 0.13
ethR 4328078 p.Leu177Arg missense_variant 0.2
ethA 4328103 c.-630C>G upstream_gene_variant 0.33
ethA 4328308 c.-835G>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408096 p.Val36Gly missense_variant 0.15
gid 4408307 c.-105G>C upstream_gene_variant 0.12