TB-Profiler result

Run: SRR14088363
Summary

Run ID: SRR14088363

Sample name:

Date: 03-04-2023 09:45:47

Number of reads: 830059

Percentage reads mapped: 97.69

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 2155850 p.Gln88* stop_gained 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576488 p.Val381Leu missense_variant 0.11
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760394 c.588C>T synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762523 p.Pro906Gln missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764541 p.Val391Gly missense_variant 0.14
rpoC 764543 p.Thr392Asp missense_variant 0.14
rpoC 765245 p.Val626Phe missense_variant 0.22
rpoC 766309 c.2940G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.12
mmpL5 776021 c.2460G>C synonymous_variant 0.12
mmpL5 776057 c.2424G>T synonymous_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776433 p.Ser683Leu missense_variant 0.2
mmpL5 776446 p.Ala679Thr missense_variant 0.18
mmpL5 778705 c.-225C>A upstream_gene_variant 0.12
mmpR5 779156 c.169delG frameshift_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800940 c.132C>A synonymous_variant 0.14
fbiC 1303331 p.Arg134Leu missense_variant 0.15
fbiC 1303383 c.453G>T synonymous_variant 0.15
fbiC 1303452 c.522G>A synonymous_variant 0.22
fbiC 1303463 p.Ala178Glu missense_variant 0.18
Rv1258c 1407133 p.Gly70Arg missense_variant 1.0
atpE 1461284 c.240C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472899 n.1054C>A non_coding_transcript_exon_variant 0.18
rrl 1475056 n.1399A>T non_coding_transcript_exon_variant 0.4
inhA 1674388 p.Leu63Phe missense_variant 0.2
inhA 1674594 c.393C>T synonymous_variant 0.18
inhA 1674981 c.780C>T synonymous_variant 0.14
rpsA 1834564 c.1023C>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918597 p.Trp220Arg missense_variant 0.11
ndh 2102745 p.Val100Phe missense_variant 0.18
katG 2154345 c.1767C>T synonymous_variant 0.13
katG 2154685 p.Ala476Glu missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167717 c.2896T>C synonymous_variant 0.15
PPE35 2167852 p.Asn921His missense_variant 0.14
PPE35 2167878 p.Ser912Asn missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2222967 c.198G>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289356 c.-115G>C upstream_gene_variant 0.18
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2986693 c.-146C>A upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087819 c.1000C>A synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474388 p.Phe128Ile missense_variant 0.25
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 1.0
whiB7 3568485 c.195T>C synonymous_variant 0.13
ddn 3986743 c.-101G>T upstream_gene_variant 0.13
clpC1 4039508 c.1197G>C synonymous_variant 0.25
clpC1 4039805 c.900C>A synonymous_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.11
embC 4241100 p.Val413Glu missense_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244944 p.Ala571Asp missense_variant 0.18
embA 4245486 p.Pro752Thr missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.21
embB 4247098 c.585C>G synonymous_variant 0.12
aftB 4267095 p.Pro581Gln missense_variant 0.14
aftB 4269024 c.-188G>A upstream_gene_variant 1.0
aftB 4269099 c.-263G>T upstream_gene_variant 0.2
ubiA 4269134 c.699delC frameshift_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.18
ethR 4326970 c.-579G>T upstream_gene_variant 0.18
ethR 4327934 p.Ala129Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0