TB-Profiler result

Run: ERR2229164

Summary

Run ID: ERR2229164

Sample name:

Date: 31-03-2023 16:46:30

Number of reads: 975358

Percentage reads mapped: 99.11

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
gyrB 6623 p.Ser462Thr missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576499 c.1152G>T synonymous_variant 0.12
rpoB 759753 c.-54C>T upstream_gene_variant 0.12
rpoB 760919 c.1113C>A synonymous_variant 0.13
rpoB 762745 p.Gln980Arg missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776218 p.Ala755Ser missense_variant 0.15
mmpL5 777164 c.1317C>T synonymous_variant 0.14
mmpL5 778414 p.Phe23Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801152 p.Thr115Met missense_variant 0.25
fbiC 1303523 p.Trp198Leu missense_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303784 p.Gly285Glu missense_variant 0.14
fbiC 1304491 c.1561_1562insGT frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474459 n.802C>G non_coding_transcript_exon_variant 0.2
rrl 1474975 n.1318G>T non_coding_transcript_exon_variant 0.29
rrl 1476004 n.2347G>T non_coding_transcript_exon_variant 0.18
rrl 1476692 n.3037delG non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167709 c.2904C>T synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169049 p.Ile522Phe missense_variant 0.25
PPE35 2169890 c.723C>T synonymous_variant 0.17
PPE35 2169893 c.720C>A synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2169910 p.Asn235Tyr missense_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.35
Rv1979c 2222199 c.966T>C synonymous_variant 0.13
Rv1979c 2223101 p.Leu22Ile missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.16
kasA 2519140 c.1026G>C synonymous_variant 0.27
kasA 2519143 c.1029G>C synonymous_variant 0.27
folC 2746141 c.1457dupC frameshift_variant 0.14
thyX 3067340 c.606G>A synonymous_variant 0.12
thyA 3074418 c.54A>G synonymous_variant 0.1
thyA 3074603 c.-132G>A upstream_gene_variant 0.12
whiB7 3568557 c.123A>G synonymous_variant 0.1
rpoA 3877699 p.His270Arg missense_variant 0.13
rpoA 3877824 p.Glu228Asp missense_variant 0.12
rpoA 3878483 c.25C>T synonymous_variant 0.15
panD 4044183 p.Met33Ile missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243704 p.Gly158Ser missense_variant 0.12
embA 4244565 p.Arg445Cys missense_variant 0.13
embA 4244835 c.1603C>T synonymous_variant 0.22
embA 4245048 p.Tyr606His missense_variant 0.11
embA 4245994 p.Ala921Glu missense_variant 0.15
embB 4246203 c.-311C>A upstream_gene_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4246721 p.Pro70Thr missense_variant 0.12
embB 4248629 p.Pro706Thr missense_variant 0.14
aftB 4268091 p.Lys249Arg missense_variant 0.12
ethA 4327310 p.Ser55Tyr missense_variant 0.15
ethA 4327926 c.-453G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0