TB-Profiler result

Run: SRR6855956
Summary

Run ID: SRR6855956

Sample name:

Date: 04-04-2023 17:51:10

Number of reads: 841197

Percentage reads mapped: 99.04

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 5078 c.-162_-161insG upstream_gene_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576692 p.Asn449His missense_variant 0.11
ccsA 619916 p.Gly9Val missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767236 p.Glu1289Asp missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777046 p.Ser479Pro missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rplC 801193 p.Arg129Trp missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473598 n.-60A>G upstream_gene_variant 0.11
rrl 1473657 n.-1T>A upstream_gene_variant 0.11
inhA 1674230 p.Ile10Thr missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155476 c.636T>G synonymous_variant 0.12
katG 2156521 c.-410C>G upstream_gene_variant 0.11
PPE35 2169943 p.Leu224Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746253 p.Asp449Gly missense_variant 0.1
pepQ 2859332 p.Thr363Ala missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449427 c.924G>C synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840205 p.Glu406* stop_gained 0.12
ddn 3986660 c.-184C>T upstream_gene_variant 0.11
ddn 3986781 c.-63C>A upstream_gene_variant 0.11
ddn 3986895 p.Ile18Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243826 c.594G>T synonymous_variant 0.1
embA 4244759 c.1527C>T synonymous_variant 0.12
embA 4245081 p.Ala617Ser missense_variant 0.14
embA 4245114 p.Gly628Cys missense_variant 0.17
embA 4245185 c.1953G>T synonymous_variant 0.12
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268704 p.Asn45Asp missense_variant 0.11
ubiA 4269881 c.-48G>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0