TB-Profiler result

Run: ERR2514345
Summary

Run ID: ERR2514345

Sample name:

Date: 31-03-2023 20:16:50

Number of reads: 1573700

Percentage reads mapped: 94.25

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 0.58 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.44
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.38
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.38
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.33
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.33
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.29
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.29
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.33
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.33
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.33
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.43
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.46
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.46
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.54
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.54
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.44
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.38
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.15
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.15
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.15
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.13
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.13
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.13
rrl 1475900 n.2243A>C non_coding_transcript_exon_variant 0.12
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.17
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.18
rrl 1475938 n.2281C>A non_coding_transcript_exon_variant 0.22
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.22
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.22
rrl 1475954 n.2297A>G non_coding_transcript_exon_variant 0.2
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.2
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.2
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.33
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.33
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.43
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.38
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.38
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.38
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.36
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.26
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0