TB-Profiler result

Run: SRR19392994
Summary

Run ID: SRR19392994

Sample name:

Date: 03-04-2023 21:37:03

Number of reads: 592993

Percentage reads mapped: 99.57

Strain: lineage4.6.1;lineage3.1.1;lineage1.1.2

Drug-resistance: HR-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
lineage3 East-African-Indian CAS RD750 0.28
lineage4 Euro-American LAM;T;S;X;H None 0.62
lineage1 Indo-Oceanic EAI RD239 0.09
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.09
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.07
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.08
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.06
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.51
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
katG 2155965 c.146dupA frameshift_variant 0.13 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
gyrB 6112 p.Met291Ile missense_variant 0.35
gyrB 6124 c.885C>T synonymous_variant 0.38
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.38
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.29
gyrA 9143 c.1842T>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.43
mshA 575907 p.Ala187Val missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 0.28
rpoB 760948 p.Asn381Ser missense_variant 0.57
rpoC 762434 c.-936T>G upstream_gene_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.3
rpoC 763884 p.Ala172Val missense_variant 0.28
rpoC 763886 c.517C>A synonymous_variant 0.29
rpoC 766024 p.Ile885Met missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.41
mmpL5 777801 p.Ile227Thr missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406088 p.Ala418Val missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 0.16
embR 1417019 p.Cys110Tyr missense_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673283 c.-157A>C upstream_gene_variant 0.1
rpsA 1833972 p.Leu144Pro missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.63
katG 2155557 c.555C>T synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 0.39
PPE35 2167983 p.Gly877Asp missense_variant 0.16
Rv1979c 2221783 p.Ala461Glu missense_variant 0.16
Rv1979c 2222308 p.Asp286Gly missense_variant 0.11
Rv1979c 2222869 p.Ala99Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.13
pncA 2289365 c.-125delC upstream_gene_variant 0.25
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26
ahpC 2726105 c.-88G>A upstream_gene_variant 0.13
ahpC 2726672 c.480G>A synonymous_variant 0.23
Rv2752c 3064532 p.Thr554Ala missense_variant 0.5
Rv2752c 3064632 c.1560C>T synonymous_variant 0.21
Rv2752c 3064674 c.1518C>T synonymous_variant 0.12
Rv2752c 3064967 p.Leu409Met missense_variant 0.11
Rv2752c 3065698 p.Ile165Thr missense_variant 0.11
Rv2752c 3065711 p.Gly161Ser missense_variant 0.33
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.13
thyX 3067231 p.Thr239Ala missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.36
Rv3083 3448714 p.Asp71His missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.36
embC 4241042 p.Asn394Asp missense_variant 0.21
embC 4241562 p.Arg567His missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.14
embA 4243848 p.Val206Met missense_variant 0.12
embA 4245149 c.1917C>T synonymous_variant 0.13
embA 4245883 p.Gly884Asp missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 0.1
embB 4247646 p.Glu378Ala missense_variant 0.18
embB 4248527 p.Phe672Leu missense_variant 0.11
aftB 4267531 p.Ala436Ser missense_variant 0.1
aftB 4269606 c.-770T>C upstream_gene_variant 0.11
ethA 4328329 c.-856C>G upstream_gene_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.14
gid 4407588 c.615A>G synonymous_variant 0.47
gid 4407873 c.330G>T synonymous_variant 0.24