TB-Profiler result

Run: ERR1035353
Summary

Run ID: ERR1035353

Sample name:

Date: 31-03-2023 10:12:15

Number of reads: 3477215

Percentage reads mapped: 94.49

Strain: lineage4.4.1.2

Drug-resistance: MDR-TB

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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 0.99
lineage4.4.1 Euro-American (S-type) S;T None 0.98
lineage4.4.1.2 Euro-American T1 None 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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rrs 1472361 n.516C>T non_coding_transcript_exon_variant 0.12 streptomycin
fabG1 1673432 c.-8T>G upstream_gene_variant 0.21 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288764 p.Thr160Pro missense_variant 0.93 pyrazinamide
embB 4247663 p.Tyr384Asn missense_variant 0.17 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 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
gyrB 5063 c.-177C>T upstream_gene_variant 0.14
gyrB 6060 p.Ser274Asn missense_variant 0.17
gyrA 6637 c.-665T>C upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7404 p.Val35Leu missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8047 p.Gly249Asp missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575302 c.-46C>T upstream_gene_variant 0.11
mshA 576181 p.Lys278Asn missense_variant 0.12
mshA 576319 c.972G>A synonymous_variant 0.18
rpoB 761190 p.Ala462Thr missense_variant 0.13
rpoC 766519 c.3150C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776231 c.2250G>A synonymous_variant 0.19
mmpL5 776532 p.Ala650Val missense_variant 0.12
mmpL5 777379 p.Leu368Phe missense_variant 0.33
mmpL5 777662 c.819C>T synonymous_variant 0.12
mmpL5 778180 p.Leu101Phe missense_variant 0.22
mmpL5 778195 p.Glu96* stop_gained 0.2
mmpL5 778344 p.Leu46Pro missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801061 p.Arg85Trp missense_variant 0.2
rplC 801115 p.Ala103Ser missense_variant 0.15
fbiC 1302807 c.-124G>A upstream_gene_variant 0.14
fbiC 1302893 c.-38G>A upstream_gene_variant 0.13
fbiC 1303016 p.Val29Gly missense_variant 0.23
fbiC 1304307 c.1377T>C synonymous_variant 0.12
fbiC 1305102 c.2172C>T synonymous_variant 0.11
fbiC 1305285 p.Gln785His missense_variant 0.11
Rv1258c 1406559 p.Gly261Val missense_variant 0.1
Rv1258c 1407079 p.Gly88Ser missense_variant 0.14
Rv1258c 1407191 c.150G>A synonymous_variant 0.14
Rv1258c 1407347 c.-7G>A upstream_gene_variant 0.29
embR 1416468 p.Asp294Asn missense_variant 0.25
atpE 1461053 c.9C>T synonymous_variant 0.14
atpE 1461193 p.Phe50Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472035 n.190G>T non_coding_transcript_exon_variant 0.15
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.14
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.11
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.29
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.38
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.39
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.53
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.16
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.17
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.12
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.15
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.17
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.38
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.24
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.24
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.24
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.24
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.15
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.11
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.16
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.15
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.17
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.12
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.14
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.21
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.21
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.21
rrl 1475289 n.1632G>A non_coding_transcript_exon_variant 0.14
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.14
rrl 1475297 n.1640C>T non_coding_transcript_exon_variant 0.15
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.16
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.13
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.15
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.13
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1476017 n.2360G>A non_coding_transcript_exon_variant 0.15
rrl 1476415 n.2758C>T non_coding_transcript_exon_variant 0.15
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.13
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.31
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.27
fabG1 1673461 p.Gly8Trp missense_variant 0.2
rpsA 1833426 c.-116T>C upstream_gene_variant 0.15
rpsA 1833966 p.Ile142Thr missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102773 c.270C>A synonymous_variant 0.12
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154236 p.Val626Met missense_variant 0.18
katG 2156027 p.Pro29Thr missense_variant 0.12
PPE35 2167770 p.Ser948Ile missense_variant 1.0
PPE35 2168831 c.1782C>A synonymous_variant 0.14
PPE35 2169020 c.1593G>T synonymous_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.44
PPE35 2170407 p.Ala69Val missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518239 p.Gly42Asp missense_variant 0.14
ahpC 2726010 c.-183G>A upstream_gene_variant 0.12
folC 2746660 c.938delT frameshift_variant 0.12
pepQ 2859548 p.Gly291Cys missense_variant 0.12
pepQ 2859964 p.Ala152Val missense_variant 0.14
pepQ 2860213 p.Pro69Leu missense_variant 0.95
ribD 2987228 p.Met130Ile missense_variant 0.14
Rv2752c 3064761 c.1431C>T synonymous_variant 0.15
Rv2752c 3066007 p.Pro62Leu missense_variant 0.15
Rv2752c 3066170 p.Pro8Ser missense_variant 0.13
Rv2752c 3066299 c.-108C>T upstream_gene_variant 0.18
Rv2752c 3066354 c.-163G>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087776 c.957G>A synonymous_variant 0.12
fbiD 3339702 c.585G>A synonymous_variant 0.12
fbiD 3339730 p.Pro205Ser missense_variant 0.12
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448859 p.Ala119Glu missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474376 p.Ala124Thr missense_variant 0.14
Rv3236c 3611992 c.1125T>C synonymous_variant 0.12
Rv3236c 3612401 p.Ser239Leu missense_variant 0.11
fbiB 3641543 c.9C>T synonymous_variant 0.18
fbiB 3641628 p.Ala32Thr missense_variant 0.13
fbiB 3641643 p.Ala37Thr missense_variant 0.12
fbiB 3641660 c.126C>T synonymous_variant 0.14
fbiB 3641679 p.Thr49Ser missense_variant 0.12
fbiB 3641721 p.Ala63Thr missense_variant 0.14
fbiB 3641727 p.Glu65Lys missense_variant 0.14
fbiB 3642101 c.567C>T synonymous_variant 0.17
alr 3841516 c.-96G>A upstream_gene_variant 0.2
ddn 3986775 c.-69A>T upstream_gene_variant 0.25
clpC1 4038295 p.Val804Met missense_variant 0.22
clpC1 4039046 c.1659C>T synonymous_variant 0.18
clpC1 4039751 p.Gln318His missense_variant 0.11
panD 4044059 p.Ala75Thr missense_variant 0.11
embC 4240988 p.Ala376Thr missense_variant 0.14
embC 4241723 p.Val621Met missense_variant 0.14
embC 4241743 c.1881C>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244476 p.Ala415Val missense_variant 0.12
embA 4245787 p.Ala852Val missense_variant 0.22
embB 4246711 c.198C>T synonymous_variant 0.2
embB 4248399 p.Leu629Pro missense_variant 0.13
embB 4248820 c.2307C>T synonymous_variant 0.14
embB 4249012 c.2499G>A synonymous_variant 1.0
embB 4249405 c.2892C>T synonymous_variant 0.13
embB 4249408 c.2895G>A synonymous_variant 0.13
aftB 4267143 p.Ala565Val missense_variant 0.12
ubiA 4269173 p.Val221Ile missense_variant 0.14
aftB 4269594 c.-758A>G upstream_gene_variant 0.11
whiB6 4338334 p.Ala63Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407630 c.573T>C synonymous_variant 0.1
gid 4408384 c.-182G>A upstream_gene_variant 0.12