TB-Profiler result

Run: SRR22528547

Summary

Run ID: SRR22528547

Sample name:

Date: 04-04-2023 04:18:31

Number of reads: 676374

Percentage reads mapped: 99.75

Strain: lineage4.4.1.1

Drug-resistance: MDR-TB


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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6748 c.-554G>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8116 p.Thr272Ile missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491002 p.Val74Met missense_variant 0.11
mshA 576113 c.769delG frameshift_variant 0.18
rpoB 761528 p.Asp574Glu missense_variant 1.0
rpoC 762590 c.-780C>T upstream_gene_variant 0.11
rpoB 763212 p.Gly1136Ser missense_variant 0.11
rpoC 764537 p.Pro390Thr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778282 c.198delC frameshift_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303820 p.Ala297Asp missense_variant 0.11
fbiC 1305203 c.2277dupC frameshift_variant 0.15
fbiC 1305458 c.2530delG frameshift_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472422 n.577T>A non_coding_transcript_exon_variant 0.18
rrl 1476582 n.2925T>C non_coding_transcript_exon_variant 0.2
fabG1 1673845 p.Ile136Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154177 c.1935G>A synonymous_variant 0.11
PPE35 2167769 c.2844C>T synonymous_variant 0.14
PPE35 2169669 p.Gly315Val missense_variant 0.14
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2222724 c.441G>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290117 c.-876C>A upstream_gene_variant 0.12
eis 2714456 p.Gly293Ser missense_variant 0.12
eis 2714889 c.444C>T synonymous_variant 0.12
folC 2746923 p.Gly226Ser missense_variant 0.14
folC 2747594 p.Asn2Ile missense_variant 0.12
Rv2752c 3064660 c.1531delG frameshift_variant 0.12
Rv2752c 3064728 c.1464T>A synonymous_variant 0.17
Rv2752c 3066261 c.-70G>A upstream_gene_variant 0.11
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448384 c.-119delC upstream_gene_variant 0.15
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473976 c.-31C>T upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641612 c.78C>A synonymous_variant 0.11
rpoA 3878417 p.Gly31Ser missense_variant 0.18
rpoA 3878630 c.-123G>C upstream_gene_variant 0.17
embC 4240557 p.Ala232Val missense_variant 0.11
embC 4241596 c.1734G>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244970 c.1738C>T synonymous_variant 1.0
embB 4248437 p.Thr642Ala missense_variant 1.0
ethR 4326703 c.-846T>C upstream_gene_variant 1.0
ethR 4327822 p.Glu92Lys missense_variant 0.13
whiB6 4338514 p.Tyr3Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0