TB-Profiler result

Run: SRR19415697
Summary

Run ID: SRR19415697

Sample name:

Date: 03-04-2023 21:37:41

Number of reads: 2112885

Percentage reads mapped: 99.62

Strain: lineage4.2.2.2;lineage3.1.1;lineage2.2.1;lineage1

Drug-resistance: Other

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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 0.34
lineage2 East-Asian Beijing RD105 0.45
lineage4 Euro-American LAM;T;S;X;H None 0.14
lineage1 Indo-Oceanic EAI RD239 0.06
lineage4.2 Euro-American H;T;LAM None 0.09
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.41
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.38
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.1
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.32
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.38
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.08
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
gid 4407851 c.351delG frameshift_variant 0.19 streptomycin
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 8688 p.Ala463Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.92
mshA 575907 p.Ala187Val missense_variant 0.47
ccsA 620625 p.Ile245Met missense_variant 0.5
rpoB 759746 c.-61C>T upstream_gene_variant 0.27
rpoB 761489 c.1683G>A synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.91
mmpL5 776182 p.Asp767Asn missense_variant 0.61
mmpS5 779615 c.-710C>G upstream_gene_variant 0.41
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.53
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.82
PPE35 2167926 p.Leu896Ser missense_variant 0.89
PPE35 2168971 p.Ile548Val missense_variant 0.12
PPE35 2170461 p.Gly51Glu missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.18
pncA 2289365 c.-125delC upstream_gene_variant 0.3
eis 2714526 c.805_806delAC frameshift_variant 0.41
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 0.31
Rv2752c 3065711 p.Gly161Ser missense_variant 0.51
ald 3086788 c.-32T>C upstream_gene_variant 0.98
Rv3083 3448714 p.Asp71His missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.14
fprA 3475159 p.Asn385Asp missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 0.51
clpC1 4040517 p.Val63Ala missense_variant 0.13
embC 4240172 p.Val104Met missense_variant 0.13
embC 4241562 p.Arg567His missense_variant 0.23
embC 4242075 p.Arg738Gln missense_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.35
embA 4245969 p.Pro913Ser missense_variant 0.12
aftB 4267300 p.Pro513Ser missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 0.5
aftB 4269606 c.-770T>C upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 0.8
gid 4407927 p.Glu92Asp missense_variant 0.31