TB-Profiler result

Run: SRR6797702
Summary

Run ID: SRR6797702

Sample name:

Date: 04-04-2023 16:15:55

Number of reads: 522249

Percentage reads mapped: 99.39

Strain: lineage3

Drug-resistance: HR-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
lineage3 East-African-Indian CAS RD750 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
katG 2155129 p.Trp328Leu missense_variant 0.18 isoniazid
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 5494 c.255G>A synonymous_variant 0.29
gyrB 5805 p.Thr189Ile missense_variant 0.15
gyrB 6582 p.Thr448Met missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8795 c.1494C>A synonymous_variant 0.12
gyrA 8948 c.1647G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760839 p.Gly345Cys missense_variant 0.12
rpoB 761491 p.Val562Glu missense_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 0.8
rpoC 762608 c.-762C>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775627 p.Trp952Arg missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776510 c.1971C>A synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801372 p.Glu188Asp missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473057 n.1212G>T non_coding_transcript_exon_variant 0.12
rrl 1475311 n.1654G>C non_coding_transcript_exon_variant 0.22
rpsA 1834100 p.Arg187Ser missense_variant 0.15
rpsA 1834434 p.Pro298Gln missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101770 p.Arg425Ser missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168008 p.Ile869Phe missense_variant 0.17
PPE35 2168074 p.Pro847Thr missense_variant 0.13
PPE35 2168347 p.Val756Phe missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714304 c.1029C>T synonymous_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3066077 c.115C>A synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474901 p.Ser299Arg missense_variant 1.0
Rv3236c 3612417 p.Glu234* stop_gained 0.33
rpoA 3878486 c.21delC frameshift_variant 0.29
ddn 3987295 p.Pro151His missense_variant 0.11
clpC1 4038667 p.Gly680Cys missense_variant 0.12
clpC1 4040318 c.387C>A synonymous_variant 0.22
embC 4241032 c.1170G>T synonymous_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.92
embB 4245854 c.-660C>A upstream_gene_variant 0.2
embB 4248984 p.Pro824His missense_variant 0.12
embB 4249000 c.2487T>G synonymous_variant 1.0
aftB 4268305 p.Val178Leu missense_variant 0.17
ethA 4327528 c.-55C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0