TB-Profiler result

Run: SRR11972172
Summary

Run ID: SRR11972172

Sample name:

Date: 03-04-2023 05:30:51

Number of reads: 751292

Percentage reads mapped: 98.27

Strain: lineage1.2.1.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.99
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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
pncA 2288707 p.Ser179Arg missense_variant 0.11 pyrazinamide
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 7526 c.225G>A synonymous_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
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
mshA 576751 p.Lys468Asn missense_variant 0.4
rpoB 761384 c.1578C>A synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.89
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764343 p.Arg325His missense_variant 0.18
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 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
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 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.21
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289623 c.-382A>C upstream_gene_variant 1.0
pncA 2290056 c.-816delG upstream_gene_variant 0.15
kasA 2518017 c.-97delA upstream_gene_variant 0.11
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.95
ahpC 2726338 p.Val49Gly missense_variant 0.17
folC 2746433 p.Gly389Asp missense_variant 0.12
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 1.0
Rv3083 3449083 p.Pro194Ser missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612013 c.1104A>T synonymous_variant 0.11
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
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 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4269357 c.-521C>T upstream_gene_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269648 c.-812C>T upstream_gene_variant 0.12
ubiA 4269864 c.-32delG upstream_gene_variant 0.95
whiB6 4338361 p.Arg54Gln missense_variant 1.0
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 1.0