TB-Profiler result

Run: SRR6856013
Summary

Run ID: SRR6856013

Sample name:

Date: 04-04-2023 17:53:19

Number of reads: 479810

Percentage reads mapped: 99.5

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 2155168 p.Ser315Thr missense_variant 1.0 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 6124 c.888delG frameshift_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8014 p.Gln238Pro missense_variant 0.11
gyrA 9287 c.1986G>A synonymous_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491262 c.481delT frameshift_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620479 p.Leu197Ile missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764043 p.Thr225Asn missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775811 p.Phe890Leu missense_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777509 c.972G>A synonymous_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 0.92
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304668 p.Ser580Pro missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461208 p.Ile55Asn missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473845 n.188G>A non_coding_transcript_exon_variant 0.18
rrl 1474683 n.1026C>T non_coding_transcript_exon_variant 0.1
rrl 1475062 n.1405A>G non_coding_transcript_exon_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834629 p.Lys363Arg missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918612 p.Val225Ile missense_variant 0.11
tlyA 1918718 p.Val260Glu missense_variant 0.11
ndh 2101796 p.Ser416Trp missense_variant 0.12
ndh 2102064 p.Glu327Lys missense_variant 0.11
ndh 2102269 c.774C>G synonymous_variant 0.15
ndh 2102909 p.Arg45Leu missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154955 p.Val386Ala missense_variant 0.11
katG 2155771 p.Arg114His missense_variant 0.18
PPE35 2167917 p.Phe899Ser missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168592 p.Pro674Leu missense_variant 0.2
PPE35 2168724 c.1888dupA frameshift_variant 0.13
PPE35 2169389 c.1223dupA frameshift_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170221 p.Pro131His missense_variant 0.14
PPE35 2170603 p.Ser4Pro missense_variant 0.13
Rv1979c 2221854 p.Ile437Met missense_variant 0.11
Rv1979c 2222111 p.Ser352Pro missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290039 c.-798C>A upstream_gene_variant 1.0
eis 2715262 p.Phe24Ser missense_variant 0.14
Rv2752c 3065825 c.366delA frameshift_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087739 p.Lys307Arg missense_variant 0.12
Rv3083 3449790 p.Cys429* stop_gained 0.13
Rv3083 3449989 c.1487delG frameshift_variant&stop_lost&splice_region_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474289 p.Glu95Lys missense_variant 0.12
fprA 3474577 p.Ile191Val missense_variant 0.12
fprA 3474626 p.Phe207Tyr missense_variant 0.18
Rv3236c 3612100 p.Ile339Met missense_variant 0.15
Rv3236c 3612349 c.768A>G synonymous_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641788 p.Val85Ala missense_variant 0.18
rpoA 3878125 p.Leu128Arg missense_variant 0.13
clpC1 4040760 c.-56C>T upstream_gene_variant 0.17
embC 4240380 p.Gln173Leu missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244536 p.Gly435Asp missense_variant 0.12
embA 4245834 c.2603_2609delTGGTGGT frameshift_variant 0.11
embA 4245844 p.Val871Glu missense_variant 0.1
embA 4245846 p.Ser872Thr missense_variant 0.1
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4247732 p.Ile407Val missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338654 c.-134_-133insC upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0