TB-Profiler result

Run: SRR12199403
Summary

Run ID: SRR12199403

Sample name:

Date: 03-04-2023 06:37:47

Number of reads: 550210

Percentage reads mapped: 97.22

Strain: lineage1.2.1.2.1

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
lineage1 Indo-Oceanic EAI RD239 0.95
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.91
lineage1.2.1.2 Indo-Oceanic NA RD239 0.94
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.85
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7973 c.672A>G synonymous_variant 0.4
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 0.69
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoB 759638 c.-169_-168insA upstream_gene_variant 0.89
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763083 p.Arg1093Ser missense_variant 0.22
rpoC 763531 c.162G>C synonymous_variant 0.34
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 0.91
embR 1417019 p.Cys110Tyr missense_variant 0.75
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.17
fabG1 1673361 c.-79C>G upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
inhA 1674162 c.-40C>T upstream_gene_variant 0.75
inhA 1674413 p.Leu71Arg missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.11
PPE35 2169901 p.Gly238Trp missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.4
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289524 c.-283C>T upstream_gene_variant 0.92
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518613 p.Pro167Ser missense_variant 0.47
kasA 2519048 p.Gly312Ser missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 0.72
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.67
fprA 3475159 p.Asn385Asp missense_variant 0.51
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612091 c.1026G>A synonymous_variant 0.5
Rv3236c 3612127 c.990C>T synonymous_variant 0.12
fbiB 3640557 c.-978T>C upstream_gene_variant 0.85
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 0.83
embA 4244420 c.1188G>C synonymous_variant 0.83
embA 4245969 p.Pro913Ser missense_variant 0.88
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.54
ubiA 4269387 p.Glu149Asp missense_variant 0.69
aftB 4269606 c.-770T>C upstream_gene_variant 0.71
ubiA 4269864 c.-32delG upstream_gene_variant 0.8
whiB6 4338361 p.Arg54Gln missense_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.79