TB-Profiler result

Run: SRR1002683
Summary

Run ID: SRR1002683

Sample name:

Date: 02-04-2023 14:19:38

Number of reads: 812987

Percentage reads mapped: 90.95

Strain: lineage4.2.1.1

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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8033 p.Tyr244* stop_gained 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575210 c.-137delG upstream_gene_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776761 p.Phe574Leu missense_variant 0.1
mmpL5 777128 c.1353A>G synonymous_variant 0.1
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102587 c.455delT frameshift_variant 0.11
katG 2154563 p.Val517Phe missense_variant 0.12
PPE35 2169234 p.Leu460* stop_gained 0.15
PPE35 2169402 p.Thr404Met missense_variant 0.95
PPE35 2169488 c.1125G>C synonymous_variant 0.2
PPE35 2169491 c.1122T>C synonymous_variant 0.2
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2169910 p.Asn235Tyr missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289964 c.-723C>A upstream_gene_variant 0.17
kasA 2518879 c.765A>G synonymous_variant 0.14
kasA 2518882 c.768C>A synonymous_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.19
kasA 2519143 c.1029G>C synonymous_variant 0.19
kasA 2519338 c.1224T>C synonymous_variant 0.11
folC 2746299 p.Glu434Lys missense_variant 0.15
folC 2747417 p.Gln61Arg missense_variant 0.11
thyX 3067240 p.Ala236Thr missense_variant 0.15
thyA 3073941 c.531C>T synonymous_variant 0.11
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240711 p.Trp283Cys missense_variant 0.12
embC 4240801 c.939C>T synonymous_variant 0.17
embC 4240803 p.Tyr314Phe missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244934 p.Thr568Ala missense_variant 0.16
embB 4245722 c.-792C>T upstream_gene_variant 0.14
embB 4247426 p.Gly305Thr missense_variant 0.13
embB 4247470 c.957T>C synonymous_variant 0.17
embB 4247472 p.Phe320Tyr missense_variant 0.17
aftB 4267781 c.1056C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407907 p.Glu99Gly missense_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0