TB-Profiler result

Run: SRR5818665
Summary

Run ID: SRR5818665

Sample name:

Date: 04-04-2023 11:41:40

Number of reads: 1309532

Percentage reads mapped: 93.2

Strain: lineage4.6.5

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.5 Euro-American T;LAM 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.13 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
tlyA 1918647 p.Asn236Lys missense_variant 1.0 capreomycin
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 5489 p.Ile84Val missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777974 c.507C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.14
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.13
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.12
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.12
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.14
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.21
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.21
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.21
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.16
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.35
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.26
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.19
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.19
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.12
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.17
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.17
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.13
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.15
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.12
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.12
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.22
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.18
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.12
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.13
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.15
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.15
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.17
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.2
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.22
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.22
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.27
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.19
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.21
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.31
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.37
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.3
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.3
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.37
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.37
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.37
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.27
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.29
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.29
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.39
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.39
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.31
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.39
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.48
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.47
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.54
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.42
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.42
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.41
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.41
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.42
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
inhA 1674678 c.477C>T synonymous_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746995 p.Val202Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640346 c.-196delA upstream_gene_variant 1.0
rpoA 3878400 c.108T>C synonymous_variant 0.15
clpC1 4038332 c.2373C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0