TB-Profiler result

Run: SRR6797294

Summary

Run ID: SRR6797294

Sample name:

Date: 04-04-2023 16:05:13

Number of reads: 322261

Percentage reads mapped: 99.07

Strain:

Drug-resistance: MDR-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
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.98
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247553 p.Ser347Ile missense_variant 1.0 ethambutol
ethA 4327175 c.54_298del frameshift_variant 1.0 ethionamide
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 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8525 c.1224C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575415 p.Gly23Asp missense_variant 0.22
ccsA 620453 p.Val188Asp missense_variant 0.67
rpoB 760218 p.Thr138Ala missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763985 p.Arg206Ser missense_variant 0.29
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
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472451 n.606C>T non_coding_transcript_exon_variant 0.14
rrs 1473149 n.1304G>A non_coding_transcript_exon_variant 0.12
rpsA 1833670 c.129C>A synonymous_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 2168475 p.Pro713His missense_variant 0.25
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170234 c.378delT frameshift_variant 0.29
PPE35 2170522 p.Trp31Arg missense_variant 0.5
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746237 c.1362G>T synonymous_variant 0.4
pepQ 2860490 c.-72G>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339044 c.-74T>A upstream_gene_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449141 p.Ser213Phe missense_variant 1.0
Rv3083 3449481 p.Glu326Asp missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474460 c.456delT frameshift_variant 0.15
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612352 c.765C>T synonymous_variant 0.5
rpoA 3877665 c.843C>A synonymous_variant 0.15
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 4245969 p.Pro913Ser missense_variant 1.0
embB 4246890 p.Thr126Ile missense_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 0.71
embB 4248664 c.2151G>T synonymous_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269580 p.Pro85His missense_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338258 c.264G>T synonymous_variant 0.22
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