TB-Profiler result

Run: ERR2229702
Summary

Run ID: ERR2229702

Sample name:

Date: 31-03-2023 17:27:23

Number of reads: 535645

Percentage reads mapped: 98.68

Strain: lineage4.8

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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 0.99
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 4247471 p.Phe320Leu missense_variant 0.18 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8527 p.Arg409Gln missense_variant 0.17
gyrA 8916 p.Arg539Cys missense_variant 0.12
gyrA 9330 p.Asn677Asp missense_variant 0.33
gyrA 9383 c.2082T>C synonymous_variant 0.2
rpoB 761575 p.Phe590Tyr missense_variant 0.18
rpoB 762376 p.Ala857Asp missense_variant 0.67
rpoC 763955 p.Lys196* stop_gained 0.22
mmpL5 776303 c.2177delC frameshift_variant 0.17
mmpR5 779142 c.154dupT frameshift_variant 0.29
mmpL5 779148 c.-668C>G upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305135 c.2205C>A synonymous_variant 0.2
embR 1417258 c.90G>T synonymous_variant 0.22
atpE 1461025 c.-20C>A upstream_gene_variant 0.2
atpE 1461131 c.87T>C synonymous_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 0.2
fabG1 1673346 c.-94C>G upstream_gene_variant 0.25
fabG1 1673349 c.-91G>C upstream_gene_variant 0.21
fabG1 1673357 c.-83G>A upstream_gene_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.17
fabG1 1673361 c.-79C>G upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
rpsA 1834762 c.1221C>T synonymous_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102598 p.Gly149Ser missense_variant 0.17
katG 2155156 p.Val319Asp missense_variant 0.18
katG 2155191 c.921A>C synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168792 c.1821A>T synonymous_variant 0.13
PPE35 2169297 p.Asn439Thr missense_variant 0.17
PPE35 2169302 p.Met437Ile missense_variant 0.17
PPE35 2169313 p.Thr434Pro missense_variant 0.12
PPE35 2169381 p.Trp411Ala missense_variant 0.12
PPE35 2169581 c.1032C>G synonymous_variant 0.12
PPE35 2169587 c.1026G>A synonymous_variant 0.13
PPE35 2169602 c.1011C>A synonymous_variant 0.25
PPE35 2169623 c.990T>C synonymous_variant 0.14
PPE35 2169643 p.Ala324Ser missense_variant 0.17
PPE35 2169650 c.963A>G synonymous_variant 0.17
PPE35 2169719 c.894C>G synonymous_variant 0.22
PPE35 2169725 c.888T>C synonymous_variant 0.3
PPE35 2170001 c.612C>T synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.72
PPE35 2170053 p.Thr187Ser missense_variant 0.72
PPE35 2170147 p.Ser156Ala missense_variant 0.13
Rv1979c 2221940 p.Arg409* stop_gained 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.18
ahpC 2726434 p.Gln81Leu missense_variant 0.17
ahpC 2726456 c.264C>T synonymous_variant 0.17
ahpC 2726704 p.Asp171Ala missense_variant 0.22
folC 2746207 c.1392C>T synonymous_variant 0.29
folC 2747761 c.-163A>T upstream_gene_variant 0.33
ribD 2986799 c.-40G>A upstream_gene_variant 0.2
ribD 2986827 c.-12G>T upstream_gene_variant 0.14
Rv2752c 3064717 p.Leu492Gln missense_variant 0.25
Rv2752c 3065687 p.Gly169Cys missense_variant 0.4
Rv2752c 3066082 p.Leu37Pro missense_variant 0.25
thyX 3068015 c.-70T>G upstream_gene_variant 0.19
thyA 3074613 c.-142C>A upstream_gene_variant 0.4
fbiD 3339364 p.Pro83Ala missense_variant 0.22
fbiD 3339674 p.Arg186Leu missense_variant 0.17
fbiA 3641336 p.Val265Ala missense_variant 0.2
ddn 3986942 p.Asp33Glu missense_variant 0.25
clpC1 4039508 c.1197G>C synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243429 p.Ala66Glu missense_variant 0.29
embA 4244210 c.978G>A synonymous_variant 0.22
embA 4244214 p.Ala328Thr missense_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.67
embB 4246548 p.Pro12Gln missense_variant 0.8
embB 4246555 c.42G>C synonymous_variant 0.75
embB 4246556 p.Ala15Pro missense_variant 0.75
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4248772 c.2259A>G synonymous_variant 0.4
ubiA 4269916 c.-83G>T upstream_gene_variant 0.12
ethA 4328205 c.-732T>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407865 p.Glu113Gly missense_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0