TB-Profiler result

Run: ERR2229528
Summary

Run ID: ERR2229528

Sample name:

Date: 31-03-2023 17:17:12

Number of reads: 897886

Percentage reads mapped: 99.18

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 9298 p.Ser666Trp missense_variant 0.1
mshA 575426 p.Ser27Thr missense_variant 0.25
mshA 575587 c.240C>A synonymous_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576789 c.1442G>T stop_lost&splice_region_variant 0.13
rpoC 767053 p.Glu1228Asp missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775754 c.2727C>A synonymous_variant 0.18
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
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
inhA 1674431 p.Arg77Gln missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918603 p.Ser222Ala missense_variant 0.11
tlyA 1918607 p.Val223Asp missense_variant 0.14
ndh 2102098 c.944delC frameshift_variant 0.12
ndh 2103165 c.-123G>T upstream_gene_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.46
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170189 p.Glu142Gln missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290144 c.-903A>G upstream_gene_variant 0.11
kasA 2518677 c.569_574delCCGACG disruptive_inframe_deletion 0.13
kasA 2518692 p.Ala193Gly missense_variant 0.12
eis 2714615 p.Glu240Lys missense_variant 0.13
folC 2746845 p.Ala252Thr missense_variant 0.12
pepQ 2859552 c.867C>T synonymous_variant 0.12
ribD 2987329 p.Ala164Val missense_variant 0.14
thyA 3073689 c.783C>T synonymous_variant 0.17
fprA 3474198 c.192C>T synonymous_variant 0.15
fprA 3474448 p.Ala148Ser missense_variant 0.13
fbiB 3642872 p.Ile446Met missense_variant 0.12
alr 3840518 c.903G>T synonymous_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3878068 p.Val147Gly missense_variant 0.14
clpC1 4039161 p.His515Gly missense_variant 0.14
clpC1 4039169 p.Glu512Asp missense_variant 0.14
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4039730 c.975C>G synonymous_variant 0.12
clpC1 4040291 c.414G>A synonymous_variant 0.13
embA 4242394 c.-839C>T upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.75
embB 4246548 p.Pro12Gln missense_variant 0.75
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246563 p.Leu17Trp missense_variant 0.6
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4249528 c.3015C>T synonymous_variant 0.13
aftB 4267773 p.Ile355Asn missense_variant 0.12
aftB 4267852 p.Gln329Lys missense_variant 0.15
aftB 4267869 p.Ala323Gly missense_variant 0.33
ubiA 4270025 c.-192C>A upstream_gene_variant 0.13
ethR 4326937 c.-612G>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.12
gid 4407885 c.318A>C synonymous_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0