TB-Profiler result

Run: ERR2229174
Summary

Run ID: ERR2229174

Sample name:

Date: 31-03-2023 16:46:41

Number of reads: 1130592

Percentage reads mapped: 95.4

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 9327 p.Ala676Thr missense_variant 0.13
mshA 576043 c.696G>T synonymous_variant 0.15
rpoB 762697 p.Ala964Asp missense_variant 0.17
rpoC 767058 p.Thr1230Asn missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.14
mmpL5 776021 c.2460G>C synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474990 n.1333C>A non_coding_transcript_exon_variant 0.17
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
fabG1 1673983 c.548delC frameshift_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101786 c.1257G>T synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169064 p.Met517Leu missense_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.2
kasA 2518882 c.768C>A synonymous_variant 0.12
kasA 2519153 p.Ile347Val missense_variant 0.15
eis 2714275 p.Arg353Leu missense_variant 0.17
folC 2746290 p.Arg437Cys missense_variant 0.22
folC 2747459 p.Leu47Pro missense_variant 0.11
pepQ 2859557 p.Glu288Lys missense_variant 0.13
thyX 3068133 c.-188G>A upstream_gene_variant 0.13
thyX 3068139 c.-194G>T upstream_gene_variant 0.15
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474663 c.657C>T synonymous_variant 0.13
Rv3236c 3612217 c.900C>A synonymous_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.23
clpC1 4038213 p.Asp831Gly missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.14
embC 4242545 p.Glu895* stop_gained 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244212 p.Pro327His missense_variant 0.2
embA 4244683 p.Arg484His missense_variant 0.12
embA 4245551 c.2322delC frameshift_variant 0.15
embA 4245632 p.Asn800Lys missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
aftB 4266967 p.Pro624Thr missense_variant 0.13
ethR 4326889 c.-660C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0