TB-Profiler result

Run: SRR6896314
Summary

Run ID: SRR6896314

Sample name:

Date: 04-04-2023 18:02:09

Number of reads: 580344

Percentage reads mapped: 99.67

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 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
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 7236 p.Asn666Thr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490824 p.Gln14His missense_variant 0.11
ccsA 620852 c.965delG frameshift_variant 0.12
rpoB 759883 p.Val26Ala missense_variant 0.14
rpoC 762536 c.-834T>A upstream_gene_variant 0.18
rpoC 763427 p.Ile20Val missense_variant 0.11
rpoC 764520 p.Asn384Ser missense_variant 0.15
rpoC 765377 c.2011delG frameshift_variant 0.1
rpoC 766821 p.Asp1151Gly missense_variant 0.12
rpoC 767223 c.3857dupC frameshift_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpR5 778154 c.-836G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781621 p.Thr21Asn missense_variant 0.11
fbiC 1304623 p.Cys565Ser missense_variant 0.12
fbiC 1304788 p.Ala620Ser missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674181 c.742T>C stop_lost&splice_region_variant 0.11
inhA 1674645 p.Asp148Glu missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102892 p.Phe51Ile missense_variant 0.12
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154881 p.Ala411Thr missense_variant 0.14
PPE35 2167699 p.Asn972Asp missense_variant 0.11
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2168508 p.Val702Ala missense_variant 0.13
PPE35 2168530 p.Gly695Cys missense_variant 0.12
PPE35 2169689 c.924C>A synonymous_variant 0.11
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518236 p.Ser41Ile missense_variant 0.17
kasA 2519129 p.Pro339Thr missense_variant 0.13
kasA 2519270 p.Ala386Ser missense_variant 0.15
eis 2714342 p.Leu331Phe missense_variant 0.25
pepQ 2859616 p.Ala268Val missense_variant 0.14
Rv2752c 3065401 p.Arg264Leu missense_variant 0.14
Rv2752c 3066042 c.150T>G synonymous_variant 0.12
thyX 3067407 p.Glu180Gly missense_variant 0.12
thyX 3067583 c.363C>T synonymous_variant 0.11
thyA 3073745 p.Tyr243His missense_variant 0.15
thyA 3073858 p.Asp205Gly missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086821 c.2T>C start_lost 0.13
fbiD 3339321 c.204G>T synonymous_variant 0.13
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449093 p.Ala197Val missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474854 p.Lys283Arg missense_variant 0.1
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3612702 p.Asp139His missense_variant 0.12
Rv3236c 3612948 p.Phe57Leu missense_variant 0.4
fbiA 3640356 c.-187G>A upstream_gene_variant 0.18
fbiB 3642609 p.Ser359Gly missense_variant 0.12
ddn 3987244 p.Gln134Arg missense_variant 0.15
clpC1 4039611 p.Arg365Pro missense_variant 0.1
clpC1 4040298 p.Gln136Pro missense_variant 0.11
embC 4239670 c.-193C>T upstream_gene_variant 0.13
embC 4241158 c.1297delG frameshift_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244226 p.Gly332Arg missense_variant 0.12
aftB 4267397 c.1440G>T synonymous_variant 0.18
aftB 4267668 p.Ala390Glu missense_variant 0.2
aftB 4267913 c.923delC frameshift_variant 0.25
ubiA 4269314 p.Lys174Glu missense_variant 0.11
ethR 4327994 c.448delG frameshift_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0