TB-Profiler result

Run: ERR1950069
Summary

Run ID: ERR1950069

Sample name:

Date: 31-03-2023 15:39:05

Number of reads: 548550

Percentage reads mapped: 99.81

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
gyrA 7607 c.307delT frameshift_variant 0.18
gyrA 9760 p.Glu820Gly missense_variant 0.11
fgd1 490663 c.-120C>T upstream_gene_variant 0.11
fgd1 491102 p.Thr107Asn missense_variant 0.13
fgd1 491764 p.Leu328Met missense_variant 0.11
mshA 575602 c.255G>A synonymous_variant 0.14
mshA 575994 p.Asn216Ser missense_variant 0.12
rpoB 762351 p.Arg849Ser missense_variant 0.12
rpoB 762696 p.Ala964Pro missense_variant 0.22
rpoC 762902 c.-468C>T upstream_gene_variant 0.15
rpoB 762931 p.Pro1042Leu missense_variant 0.11
rpoC 763519 c.150G>A synonymous_variant 0.14
rpoC 764443 c.1074C>T synonymous_variant 0.14
rpoC 765468 p.Leu700Arg missense_variant 0.12
rpoC 765676 p.Glu769Asp missense_variant 0.11
rpoC 767147 p.Ala1260Thr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777303 p.Ile393Asn missense_variant 0.13
mmpL5 777737 c.744T>C synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303553 p.Ala208Val missense_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303847 p.Phe306Ser missense_variant 0.14
fbiC 1304195 p.Thr422Asn missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472941 n.1096A>G non_coding_transcript_exon_variant 0.15
rrl 1473663 n.6A>G non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475030 n.1373G>A non_coding_transcript_exon_variant 0.17
fabG1 1674173 c.737delG frameshift_variant 0.13
rpsA 1834613 p.Ile358Val missense_variant 0.13
rpsA 1834910 p.Glu457* stop_gained 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102188 c.855G>A synonymous_variant 0.17
katG 2155158 p.Glu318Asp missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169017 p.Leu532Phe missense_variant 0.18
PPE35 2169030 p.Asp528Val missense_variant 0.15
PPE35 2169880 p.Phe245Ile missense_variant 0.29
PPE35 2170066 p.Ala183Thr missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518902 p.Ala263Val missense_variant 0.15
folC 2747752 c.-154G>A upstream_gene_variant 0.33
pepQ 2860015 p.Lys135Arg missense_variant 0.17
ribD 2986956 c.120delG frameshift_variant 0.11
ribD 2987571 p.Thr245Ala missense_variant 0.25
Rv2752c 3064930 p.Leu421Gln missense_variant 0.15
thyA 3074033 p.His147Asn missense_variant 0.18
thyA 3074374 p.Gln33Leu missense_variant 0.11
ald 3086657 c.-163T>C upstream_gene_variant 0.14
fbiD 3338938 c.-180G>C upstream_gene_variant 0.13
Rv3236c 3612126 p.Val331Ile missense_variant 0.14
Rv3236c 3612902 p.Ala72Asp missense_variant 0.12
fbiA 3640402 c.-141C>T upstream_gene_variant 0.11
rpoA 3878490 c.18C>G synonymous_variant 0.6
clpC1 4039003 p.Asn568Asp missense_variant 0.12
clpC1 4039268 c.1437C>T synonymous_variant 0.12
clpC1 4040349 p.Val119Gly missense_variant 0.17
clpC1 4040506 p.Ile67Val missense_variant 0.12
embC 4241745 p.Phe628Ser missense_variant 0.15
embC 4241774 p.Asn638Asp missense_variant 0.13
embC 4242360 p.Asn833Thr missense_variant 0.17
embC 4242516 p.Val885Glu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242737 c.2878delC frameshift_variant 0.12
embA 4244013 c.781T>C synonymous_variant 0.13
embB 4247881 c.1368G>A synonymous_variant 0.11
embB 4249447 c.2934G>A synonymous_variant 0.17
aftB 4268801 c.35delC frameshift_variant 0.22
ubiA 4268980 p.Gln285Leu missense_variant 0.25
ubiA 4269668 p.Ser56Thr missense_variant 0.14
ethR 4327096 c.-453G>A upstream_gene_variant 0.12
ethR 4327639 p.Ala31Pro missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0