TB-Profiler result

Run: SRR14802219
Summary

Run ID: SRR14802219

Sample name:

Date: 03-04-2023 12:20:49

Number of reads: 3060329

Percentage reads mapped: 90.85

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 0.26 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
mshA 576108 p.Ala254Gly missense_variant 0.25
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 1472507 n.662C>G non_coding_transcript_exon_variant 0.2
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.23
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.23
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.25
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.25
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.24
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.25
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.24
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.23
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.23
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.23
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.22
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.24
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.24
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.32
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.29
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.23
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.23
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.22
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.2
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.21
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.21
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.21
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.2
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.2
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.2
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.24
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.24
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.27
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.27
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.14
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.13
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.18
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.29
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.32
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.39
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.38
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.37
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.37
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.4
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.3
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168247 p.Leu789Arg missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289952 c.-711C>G upstream_gene_variant 1.0
thyA 3074588 c.-117A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.15
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0