TB-Profiler result

Run: SRR1002697
Summary

Run ID: SRR1002697

Sample name:

Date: 02-04-2023 14:20:03

Number of reads: 510918

Percentage reads mapped: 98.08

Strain: lineage4.2.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.99
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 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 0.13 isoniazid
katG 2155689 p.Leu141Phe missense_variant 0.22 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 6268 c.1029C>A synonymous_variant 0.12
gyrB 7087 p.Met616Ile missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7669 p.Pro123Arg missense_variant 0.18
gyrA 7672 p.Pro124Leu missense_variant 0.18
gyrA 8553 c.1252C>A synonymous_variant 0.12
gyrA 8909 p.Ser536Arg missense_variant 0.13
gyrA 8952 p.Gln551Lys missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9719 c.2418G>T synonymous_variant 0.13
fgd1 491012 p.Pro77His missense_variant 0.14
fgd1 491444 p.Ser221Tyr missense_variant 0.15
fgd1 491719 p.Pro313Thr missense_variant 0.14
rpoB 759620 c.-187A>C upstream_gene_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.12
mmpL5 776024 c.2457G>C synonymous_variant 0.12
mmpL5 776080 p.Ala801Ser missense_variant 0.25
mmpL5 776081 c.2400G>A synonymous_variant 0.25
mmpL5 777041 c.1440G>A synonymous_variant 0.15
mmpL5 777119 p.His454Gln missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.18
mmpL5 777451 p.Val344Leu missense_variant 1.0
mmpL5 777475 p.Gly336Ser missense_variant 0.14
mmpL5 777877 p.Arg202Ser missense_variant 0.29
mmpR5 778037 c.-953G>A upstream_gene_variant 0.15
mmpL5 778056 p.Ser142Asn missense_variant 0.13
mmpR5 778061 c.-929C>T upstream_gene_variant 0.12
mmpL5 778064 p.Ala139Val missense_variant 0.12
mmpL5 778070 p.Thr137Ala missense_variant 0.12
mmpR5 778079 c.-911C>G upstream_gene_variant 0.13
mmpR5 778085 c.-905A>G upstream_gene_variant 0.14
mmpR5 778385 c.-605C>A upstream_gene_variant 0.18
mmpS5 778503 p.Thr135Ala missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471647 n.-199G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475260 n.1603C>A non_coding_transcript_exon_variant 0.14
rrl 1475919 n.2262C>A non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.38
rpsA 1833454 c.-88G>T upstream_gene_variant 0.25
rpsA 1833515 c.-27C>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918710 p.Glu257Asp missense_variant 0.33
ndh 2102692 c.351C>G synonymous_variant 0.11
ndh 2102875 c.168C>T synonymous_variant 0.33
PPE35 2167865 c.2748G>C synonymous_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.15
PPE35 2169381 p.Trp411Ser missense_variant 0.13
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2222951 p.Val72Phe missense_variant 0.17
Rv1979c 2223123 c.42G>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288893 c.349C>T synonymous_variant 0.13
pncA 2289243 c.-2G>A upstream_gene_variant 0.14
kasA 2518798 c.684G>C synonymous_variant 0.29
kasA 2518801 c.687G>A synonymous_variant 0.4
kasA 2518809 p.Lys232Arg missense_variant 0.57
kasA 2518839 p.Ala242Gly missense_variant 0.22
kasA 2519041 c.927C>T synonymous_variant 0.25
eis 2715310 p.Pro8Gln missense_variant 0.67
eis 2715437 c.-105G>T upstream_gene_variant 0.67
ahpC 2726183 c.-10G>A upstream_gene_variant 0.12
pepQ 2860121 p.His100Asn missense_variant 0.22
Rv2752c 3065032 p.Gly387Val missense_variant 0.17
Rv2752c 3065035 p.Asn386Ser missense_variant 0.15
thyX 3067226 p.Glu240Asp missense_variant 0.18
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448888 c.385C>A synonymous_variant 0.18
Rv3083 3449934 c.1431C>A synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474881 p.Asn292Ser missense_variant 0.12
alr 3840300 p.Pro374Leu missense_variant 0.13
alr 3840490 p.Pro311Thr missense_variant 0.13
alr 3840923 c.498C>T synonymous_variant 0.22
alr 3841009 p.Leu138Ile missense_variant 0.33
alr 3841022 c.399C>A synonymous_variant 0.29
alr 3841546 c.-126C>A upstream_gene_variant 0.33
clpC1 4039594 p.Arg371Gly missense_variant 0.22
clpC1 4039610 c.1095G>C synonymous_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.22
clpC1 4040272 p.Tyr145His missense_variant 0.18
embC 4241300 p.Ala480Ser missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245296 c.2064G>C synonymous_variant 0.13
embA 4245974 p.Ile914Met missense_variant 0.5
embB 4247426 p.Gly305Thr missense_variant 0.2
embB 4249370 p.Leu953Met missense_variant 0.22
embB 4249386 p.Glu958Gly missense_variant 0.25
embB 4249702 c.3189C>T synonymous_variant 0.22
ethR 4326982 c.-567C>G upstream_gene_variant 0.12
ethA 4327002 p.Val158Phe missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338630 c.-109C>T upstream_gene_variant 0.12
gid 4408213 c.-11C>T upstream_gene_variant 1.0