TB-Profiler result

Run: SRR6896442
Summary

Run ID: SRR6896442

Sample name:

Date: 04-04-2023 18:06:07

Number of reads: 300731

Percentage reads mapped: 99.59

Strain: lineage4.4.1.1

Drug-resistance: Sensitive

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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
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 5054 c.-186G>T upstream_gene_variant 0.17
gyrB 6070 c.835delT frameshift_variant 0.12
gyrB 6608 p.Val457Ile missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762765 c.-605C>T upstream_gene_variant 0.25
rpoC 764374 p.Phe335Leu missense_variant 0.22
rpoC 764803 c.1434C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpL5 778165 p.His106Asn missense_variant 0.17
mmpR5 779449 p.Leu154Met missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303840 p.Ala304Ser missense_variant 0.12
fbiC 1303961 p.Arg344Gln missense_variant 0.12
embR 1417008 c.339delG frameshift_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471729 n.-117T>C upstream_gene_variant 0.12
rrs 1472714 n.873delC non_coding_transcript_exon_variant 0.12
rrs 1473361 n.1516G>T non_coding_transcript_exon_variant 0.12
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 0.13
rrl 1474221 n.564T>A non_coding_transcript_exon_variant 0.13
rrl 1475188 n.1531C>A non_coding_transcript_exon_variant 0.22
inhA 1673363 c.-839G>A upstream_gene_variant 1.0
inhA 1674856 p.Glu219* stop_gained 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154149 p.Asn655Asp missense_variant 0.11
katG 2155915 p.Ala66Val missense_variant 0.22
katG 2155983 c.129C>A synonymous_variant 0.18
katG 2156074 p.Thr13Asn missense_variant 0.17
katG 2156473 c.-365_-363delGAT upstream_gene_variant 0.18
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169101 c.1512G>T synonymous_variant 0.17
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2222781 c.384C>T synonymous_variant 0.14
Rv1979c 2222923 c.240_241dupCT frameshift_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715031 p.Cys101Phe missense_variant 0.15
eis 2715050 p.Gly95Cys missense_variant 0.18
ahpC 2725934 c.-259G>T upstream_gene_variant 0.11
Rv2752c 3065648 p.Pro182Thr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339666 c.549G>T synonymous_variant 0.13
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449540 p.Thr346Asn missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612221 p.Ala299Asp missense_variant 0.22
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
alr 3840274 c.1146delT frameshift_variant 0.12
rpoA 3878407 c.100dupC frameshift_variant 0.22
clpC1 4039528 c.1177C>A synonymous_variant 0.13
clpC1 4039550 c.1155G>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248474 p.Val654Ala missense_variant 0.17
embB 4249731 p.Ala1073Asp missense_variant 0.25
ethR 4328125 p.Ser193Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0