TB-Profiler result

Run: ERR2229374
Summary

Run ID: ERR2229374

Sample name:

Date: 31-03-2023 17:07:35

Number of reads: 1028113

Percentage reads mapped: 98.92

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491631 c.849C>A synonymous_variant 0.12
mshA 575413 p.Glu22Asp missense_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.37
mshA 576440 p.Cys365Arg missense_variant 0.15
ccsA 620209 c.323delG frameshift_variant 0.12
rpoB 760526 p.Glu240Asp missense_variant 0.12
rpoC 764174 p.Asp269Asn missense_variant 0.13
rpoC 765308 p.Glu647* stop_gained 0.22
rpoC 767075 p.Ala1236Ser missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775832 c.2649C>T synonymous_variant 0.25
mmpL5 775868 c.2613C>A synonymous_variant 0.29
mmpL5 776790 p.Val564Asp missense_variant 0.17
mmpL5 776821 p.Val554Phe missense_variant 0.19
mmpL5 777149 p.Asn444Lys missense_variant 0.14
mmpL5 777157 c.1324C>A synonymous_variant 0.21
mmpL5 777164 c.1317C>T synonymous_variant 0.23
mmpL5 777173 c.1308C>T synonymous_variant 0.23
mmpL5 777176 p.Glu435Asp missense_variant 0.27
mmpR5 778451 c.-539C>T upstream_gene_variant 0.12
mmpS5 778788 c.116_117delTG frameshift_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406326 c.1015C>A synonymous_variant 0.25
Rv1258c 1406711 c.630C>T synonymous_variant 0.15
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.13
Rv1258c 1406946 p.Ala132Gly missense_variant 0.13
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.13
atpE 1460908 c.-137T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472158 n.313C>A non_coding_transcript_exon_variant 0.13
rrs 1472578 n.733G>C non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474016 n.361_362delGA non_coding_transcript_exon_variant 0.17
rrl 1475304 n.1647T>A non_coding_transcript_exon_variant 0.12
rrl 1476101 n.2444C>A non_coding_transcript_exon_variant 0.21
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
inhA 1674684 p.Met161Ile missense_variant 0.25
rpsA 1834876 c.1335G>A synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102389 c.654G>C synonymous_variant 0.22
ndh 2102392 c.651C>A synonymous_variant 0.22
ndh 2102474 p.Ala190Val missense_variant 0.12
katG 2154709 p.Thr468Asn missense_variant 0.12
katG 2155351 p.Arg254Pro missense_variant 0.11
PPE35 2167745 p.Thr956Arg missense_variant 0.19
PPE35 2167865 c.2748G>C synonymous_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169209 c.1404C>A synonymous_variant 0.14
PPE35 2169269 c.1344A>G synonymous_variant 0.15
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169278 c.1335T>C synonymous_variant 0.23
PPE35 2169281 c.1332T>G synonymous_variant 0.23
PPE35 2169287 c.1326T>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.72
PPE35 2170053 p.Thr187Ser missense_variant 0.71
Rv1979c 2222197 p.Ala323Glu missense_variant 0.12
Rv1979c 2222317 p.Ala283Val missense_variant 0.13
Rv1979c 2223006 c.159A>G synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289102 p.Thr47Asn missense_variant 0.13
pncA 2290125 c.-884C>A upstream_gene_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.16
kasA 2519143 c.1029G>C synonymous_variant 0.16
eis 2714418 c.915C>A synonymous_variant 0.17
pepQ 2859878 p.Leu181Val missense_variant 0.4
pepQ 2859968 p.Asp151Asn missense_variant 0.18
ribD 2987451 c.614_616delGTG disruptive_inframe_deletion 0.17
ribD 2987458 c.620_621insCAC disruptive_inframe_insertion 0.15
Rv2752c 3064577 p.Lys539Glu missense_variant 0.14
thyA 3074177 c.295C>A synonymous_variant 0.17
ald 3087533 c.714C>T synonymous_variant 0.17
ald 3087754 p.Ala312Val missense_variant 0.14
Rv3236c 3612857 p.Arg87His missense_variant 0.18
fbiB 3640548 c.-987G>A upstream_gene_variant 0.14
fbiB 3641523 c.-12G>A upstream_gene_variant 0.15
alr 3840725 c.696G>A synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.22
rpoA 3878071 p.Tyr146Cys missense_variant 0.12
rpoA 3878599 c.-92C>G upstream_gene_variant 0.8
clpC1 4039360 p.Ser449Gly missense_variant 0.29
clpC1 4039645 p.His354Asp missense_variant 0.25
clpC1 4039654 p.Thr351Ser missense_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.12
embC 4240508 p.Ala216Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246046 c.-468G>T upstream_gene_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.36
embB 4246555 c.42G>C synonymous_variant 0.55
embB 4246556 p.Ala15Pro missense_variant 0.55
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4249709 p.Lys1066Glu missense_variant 0.25
aftB 4267871 p.Gln322His missense_variant 0.29
aftB 4267973 c.864G>T synonymous_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0