TB-Profiler result

Run: SRR6896317
Summary

Run ID: SRR6896317

Sample name:

Date: 04-04-2023 18:02:14

Number of reads: 738848

Percentage reads mapped: 99.15

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 0.99
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
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 8457 p.Glu386Lys missense_variant 0.12
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576776 p.Gly477Arg missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776890 p.Ser531Ala missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpL5 779250 c.-770C>G upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407508 c.-168G>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475754 n.2097G>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168065 p.Thr850Ala missense_variant 0.12
PPE35 2168448 p.Gln722Leu missense_variant 0.12
PPE35 2168475 p.Pro713His missense_variant 0.17
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169933 p.Ile227Thr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289753 c.-512T>C upstream_gene_variant 1.0
pncA 2290202 c.-961C>G upstream_gene_variant 0.12
kasA 2518106 c.-9C>G upstream_gene_variant 0.12
thyA 3074497 c.-26G>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449001 c.498G>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiA 3640350 c.-193C>A upstream_gene_variant 1.0
fbiB 3642037 p.Ala168Asp missense_variant 0.12
fbiB 3642149 c.615C>A synonymous_variant 0.12
embC 4242032 c.2173delC frameshift_variant 0.2
embC 4242196 c.2334A>C synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243411 p.Ala60Val missense_variant 0.14
embA 4243626 p.Ala132Ser missense_variant 0.12
embA 4243764 p.Lys178Glu missense_variant 0.1
embA 4244360 p.Asn376Lys missense_variant 0.11
embA 4244699 c.1467C>A synonymous_variant 0.12
embA 4244810 p.Phe526Leu missense_variant 0.18
embA 4244970 p.Leu580Met missense_variant 0.13
embB 4249808 c.3295T>C stop_lost&splice_region_variant 0.11
aftB 4267897 p.Phe314Ile missense_variant 0.17
aftB 4268340 p.Pro166Gln missense_variant 0.2
aftB 4268432 c.405C>A synonymous_variant 0.14
aftB 4268501 c.335delG frameshift_variant 0.11
aftB 4268544 p.Leu98His missense_variant 0.13
aftB 4268615 c.222C>A synonymous_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0