TB-Profiler result

Run: ERR4815948
Summary

Run ID: ERR4815948

Sample name:

Date: 01-04-2023 14:09:22

Number of reads: 485355

Percentage reads mapped: 94.67

Strain: lineage4.8

Drug-resistance: Other

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 1.0 streptomycin
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 5761 p.Trp174* stop_gained 0.14
gyrB 6590 p.Arg451Cys missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490670 c.-113G>A upstream_gene_variant 0.11
fgd1 490679 c.-104A>G upstream_gene_variant 0.11
fgd1 490687 c.-96T>C upstream_gene_variant 0.1
fgd1 490690 c.-93C>A upstream_gene_variant 0.11
fgd1 490968 c.186C>T synonymous_variant 0.1
fgd1 491494 p.Asp238Asn missense_variant 0.33
ccsA 620652 c.762C>T synonymous_variant 0.18
rpoB 759983 c.177C>T synonymous_variant 0.13
rpoB 760662 p.Ala286Thr missense_variant 0.15
rpoB 762362 c.2556G>A synonymous_variant 0.14
rpoC 766644 p.Glu1092Gly missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777484 c.996delT frameshift_variant 0.11
mmpL5 778163 p.His106Gln missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801434 p.Arg209Leu missense_variant 0.11
fbiC 1303273 p.Arg115Ser missense_variant 0.11
fbiC 1305361 p.Leu811Met missense_variant 0.11
Rv1258c 1406807 c.534G>A synonymous_variant 0.18
embR 1416198 c.1149delG frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.4
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.4
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.4
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 1.0
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 1.0
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 1.0
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 1.0
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.4
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.5
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.4
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.6
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
inhA 1674229 p.Ile10Val missense_variant 0.2
inhA 1674296 c.98delG frameshift_variant 0.2
inhA 1674453 c.252G>C synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155973 p.Val47Ile missense_variant 1.0
PPE35 2168027 c.2586C>T synonymous_variant 0.2
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2222095 p.Ala357Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519055 p.Ala314Val missense_variant 0.18
folC 2747310 p.Thr97Ser missense_variant 0.2
pepQ 2860250 p.Asp57Asn missense_variant 0.17
thyX 3067952 c.-7G>T upstream_gene_variant 0.25
thyX 3067954 c.-9G>C upstream_gene_variant 0.25
thyX 3067955 c.-10G>C upstream_gene_variant 0.25
thyX 3067957 c.-12A>C upstream_gene_variant 0.25
ald 3086625 c.-195G>A upstream_gene_variant 0.11
ald 3087700 p.Leu294Pro missense_variant 0.12
Rv3083 3448399 c.-105T>C upstream_gene_variant 0.15
fprA 3474058 p.Ala18Thr missense_variant 0.12
Rv3236c 3612279 c.838C>T synonymous_variant 0.11
Rv3236c 3612878 p.Thr80Ile missense_variant 0.12
Rv3236c 3612997 c.120T>G synonymous_variant 0.22
fbiB 3641013 c.-522C>T upstream_gene_variant 0.13
rpoA 3877760 p.Pro250Thr missense_variant 0.15
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040093 c.612C>T synonymous_variant 1.0
panD 4044435 c.-154C>A upstream_gene_variant 0.18
embC 4240801 c.939C>T synonymous_variant 0.12
embC 4240803 p.Tyr314Phe missense_variant 0.12
embC 4242074 c.2212C>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244124 p.Gly298Arg missense_variant 0.18
embA 4245167 c.1935G>C synonymous_variant 0.11
embB 4245794 c.-720G>A upstream_gene_variant 0.25
embB 4247450 p.Ala313Thr missense_variant 0.18
embB 4248229 p.Trp572* stop_gained 0.11
embB 4248536 c.2023C>T synonymous_variant 0.11
aftB 4269024 c.-188G>A upstream_gene_variant 0.12
ethA 4326159 p.Val439Met missense_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.2
ethR 4326964 c.-585G>A upstream_gene_variant 0.22
ethR 4326970 c.-579G>T upstream_gene_variant 0.36
ethR 4326982 c.-567C>G upstream_gene_variant 0.33
ethR 4327588 p.Arg15Gln missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0