TB-Profiler result

Run: SRR1180143
Summary

Run ID: SRR1180143

Sample name:

Date: 03-04-2023 03:45:29

Number of reads: 6835768

Percentage reads mapped: 99.34

Strain: lineage2.2.1;lineage1.2.2.2

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
lineage2 East-Asian Beijing RD105 0.23
lineage1 Indo-Oceanic EAI RD239 0.77
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.22
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.78
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.19
lineage1.2.2.2 Indo-Oceanic NA RD239 0.78
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 5075 c.-165C>T upstream_gene_variant 0.73
gyrB 6112 p.Met291Ile missense_variant 0.73
gyrA 7268 c.-34C>T upstream_gene_variant 0.87
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.78
gyrA 9143 c.1842T>C synonymous_variant 0.78
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 575907 p.Ala187Val missense_variant 0.31
ccsA 620625 p.Ile245Met missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763552 c.183C>T synonymous_variant 0.84
rpoC 763884 p.Ala172Val missense_variant 0.74
rpoC 763886 c.517C>A synonymous_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
mmpL5 776182 p.Asp767Asn missense_variant 0.24
mmpS5 779615 c.-710C>G upstream_gene_variant 0.21
mmpS5 779625 c.-720G>A upstream_gene_variant 0.79
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406253 p.Gly363Val missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24
embR 1417019 p.Cys110Tyr missense_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674210 c.9A>C synonymous_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.74
katG 2154724 p.Arg463Leu missense_variant 0.97
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2168742 p.Gly624Asp missense_variant 0.84
Rv1979c 2222308 p.Asp286Gly missense_variant 0.76
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.72
ahpC 2726051 c.-142G>A upstream_gene_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 0.99
Rv3083 3448714 p.Asp71His missense_variant 0.72
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.81
fprA 3475159 p.Asn385Asp missense_variant 0.71
Rv3236c 3612813 p.Thr102Ala missense_variant 0.26
clpC1 4040517 p.Val63Ala missense_variant 0.86
clpC1 4040719 c.-15A>G upstream_gene_variant 0.73
embC 4240671 p.Thr270Ile missense_variant 0.77
embC 4241042 p.Asn394Asp missense_variant 0.72
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.23
embA 4245670 p.Ala813Gly missense_variant 0.8
embA 4245969 p.Pro913Ser missense_variant 0.85
embB 4246979 p.Gly156Cys missense_variant 0.75
embB 4247646 p.Glu378Ala missense_variant 0.74
aftB 4267647 p.Asp397Gly missense_variant 0.21
aftB 4267960 p.Val293Met missense_variant 0.74
ubiA 4269387 p.Glu149Asp missense_variant 0.8
aftB 4269606 c.-770T>C upstream_gene_variant 0.81
ethA 4326148 c.1326G>T synonymous_variant 0.78
ethA 4326439 p.Asn345Lys missense_variant 0.77
whiB6 4338203 p.Arg107Cys missense_variant 0.72
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.73
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407848 p.Ala119Thr missense_variant 0.8
gid 4407873 c.330G>T synonymous_variant 0.77
gid 4407927 p.Glu92Asp missense_variant 0.18