TB-Profiler result

Run: SRR6045782
Summary

Run ID: SRR6045782

Sample name:

Date: 04-04-2023 12:05:09

Number of reads: 929255

Percentage reads mapped: 52.69

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 2155843 p.Trp90* stop_gained 0.12 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 490751 c.-32T>G upstream_gene_variant 0.21
fgd1 491604 c.822G>T synonymous_variant 0.1
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576042 p.Pro232Leu missense_variant 0.11
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764352 p.Val328Ala missense_variant 0.11
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 1416250 c.1098C>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473069 n.1224T>A non_coding_transcript_exon_variant 0.22
rrl 1473442 n.-216G>A upstream_gene_variant 1.0
inhA 1674924 c.723G>A synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101791 p.Thr418Ser missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167681 p.Ser978Thr missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170280 c.333C>G synonymous_variant 0.11
PPE35 2170298 c.315A>G synonymous_variant 0.11
Rv1979c 2222692 p.Ala158Val missense_variant 0.12
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
pncA 2289959 c.-718A>T upstream_gene_variant 0.12
kasA 2518740 p.Ala209Gly missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987357 c.519C>A synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474144 p.Trp46Cys missense_variant 0.1
fprA 3474361 p.Leu119Met missense_variant 0.11
Rv3236c 3612265 c.852G>A synonymous_variant 0.12
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244832 p.Val534Met missense_variant 0.11
aftB 4267938 p.Arg300Gln missense_variant 0.11
ubiA 4269266 p.Gly190Ser missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0