TB-Profiler result

Run: SRR5481426
Summary

Run ID: SRR5481426

Sample name:

Date: 04-04-2023 10:26:01

Number of reads: 1152519

Percentage reads mapped: 99.75

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
embB 4247231 p.Asp240His missense_variant 0.22 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 5204 c.-36C>T upstream_gene_variant 0.15
gyrB 5788 c.549G>A synonymous_variant 0.12
gyrB 5910 p.Ser224Ile missense_variant 0.17
gyrA 6817 c.-485G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7871 c.570G>T synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490697 c.-86C>T upstream_gene_variant 0.17
rpoB 760238 p.Gln144His missense_variant 0.17
rpoB 760280 c.474C>A synonymous_variant 0.33
rpoB 760283 c.477G>T synonymous_variant 0.33
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 762893 p.His1029Gln missense_variant 0.2
rpoC 764024 c.655T>C synonymous_variant 0.25
rpoC 764273 p.Phe302Leu missense_variant 0.17
rpoC 764825 p.Val486Leu missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775929 p.Asn851Ser missense_variant 0.11
mmpL5 776045 c.2436G>C synonymous_variant 0.13
mmpR5 779110 p.Gly41Ser missense_variant 0.25
mmpR5 779390 p.Arg134Leu missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.5
Rv1258c 1407326 p.Asn5Lys missense_variant 0.11
embR 1416440 c.902_907delACCCAC disruptive_inframe_deletion 0.12
embR 1416824 p.Thr175Ile missense_variant 0.18
embR 1416826 c.522T>C synonymous_variant 0.18
atpE 1460973 c.-72G>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472048 n.203T>C non_coding_transcript_exon_variant 0.13
rrs 1473196 n.1351C>A non_coding_transcript_exon_variant 0.12
rrs 1473382 n.1537T>C splice_region_variant&non_coding_transcript_exon_variant 0.11
rrl 1473680 n.23G>C non_coding_transcript_exon_variant 0.1
rrl 1473989 n.332C>A non_coding_transcript_exon_variant 0.29
rrl 1474006 n.349G>A non_coding_transcript_exon_variant 0.33
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673357 c.-83G>A upstream_gene_variant 0.23
fabG1 1673359 c.-81T>C upstream_gene_variant 0.23
fabG1 1673361 c.-79C>G upstream_gene_variant 0.23
fabG1 1673380 c.-60C>G upstream_gene_variant 0.46
rpsA 1833683 c.145dupG frameshift_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101740 p.Gln435* stop_gained 0.12
ndh 2102647 c.396C>A synonymous_variant 0.18
katG 2154133 p.Asn660Ser missense_variant 0.33
katG 2155351 p.Arg254Leu missense_variant 0.17
katG 2155927 p.Phe62Ser missense_variant 0.18
PPE35 2167812 p.Gln934Leu missense_variant 0.15
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167878 p.Ser912Asn missense_variant 0.11
PPE35 2167898 c.2715G>C synonymous_variant 0.11
PPE35 2167998 p.Pro872Leu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289359 c.-118G>T upstream_gene_variant 0.33
pncA 2289558 c.-317C>T upstream_gene_variant 0.14
kasA 2518294 c.180C>T synonymous_variant 0.13
kasA 2518780 p.Glu222Asp missense_variant 0.22
pepQ 2859827 p.Ala198Thr missense_variant 0.12
Rv2752c 3064825 p.Asp456Gly missense_variant 0.18
Rv2752c 3064988 p.Met402Val missense_variant 0.2
Rv2752c 3065728 p.Ala155Val missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074029 p.Ala148Val missense_variant 0.11
thyA 3074284 p.Leu63Ser missense_variant 0.13
ald 3086672 c.-148C>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449174 p.Asp224Gly missense_variant 0.17
fprA 3473906 c.-101A>G upstream_gene_variant 0.2
fprA 3473986 c.-21G>A upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474251 p.Val82Ala missense_variant 0.11
fprA 3474279 c.273C>A synonymous_variant 0.11
fprA 3474299 p.Asp98Gly missense_variant 0.11
fprA 3474673 p.Val223Met missense_variant 0.22
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612945 p.Ile58Phe missense_variant 0.12
fbiB 3640851 c.-684G>A upstream_gene_variant 0.13
fbiB 3640872 c.-663C>T upstream_gene_variant 1.0
fbiA 3640888 c.349delC frameshift_variant 0.12
fbiB 3642353 c.819C>A synonymous_variant 0.12
alr 3841400 c.21T>C synonymous_variant 0.29
rpoA 3877634 p.Lys292Glu missense_variant 0.2
rpoA 3878146 p.Pro121His missense_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039798 p.Asp303Asn missense_variant 0.11
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4240275 p.Pro138Leu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244189 c.957C>G synonymous_variant 0.22
embA 4244624 c.1393delC frameshift_variant 0.18
embA 4245117 p.Asn629Asp missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.23
embB 4246555 c.42G>C synonymous_variant 0.23
embB 4246556 p.Ala15Pro missense_variant 0.24
embB 4246563 p.Leu17Trp missense_variant 0.14
embB 4246567 c.54G>T synonymous_variant 0.14
embB 4248276 p.Thr588Met missense_variant 0.13
embB 4249805 p.Pro1098Thr missense_variant 0.15
aftB 4267657 p.Gly394Cys missense_variant 0.22
ethA 4326255 p.Asn407Asp missense_variant 0.25
ethA 4326413 p.Ala354Val missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408126 p.Leu26Ser missense_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 1.0