TB-Profiler result

Run: SRR6397585
Summary

Run ID: SRR6397585

Sample name:

Date: 04-04-2023 14:03:49

Number of reads: 1479805

Percentage reads mapped: 24.07

Strain: lineage4.4.1.2

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
lineage4.4 Euro-American S;T None 0.98
lineage4.4.1 Euro-American (S-type) S;T None 0.98
lineage4.4.1.2 Euro-American T1 None 0.96
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 0.35 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779565 c.-660G>C upstream_gene_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471658 n.-188T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.15
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.15
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.15
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.18
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.3
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.36
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.34
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.35
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.36
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.37
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.4
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.39
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.38
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.38
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.38
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.28
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.28
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.31
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.18
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.14
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.17
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.46
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.49
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.5
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.5
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.52
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.51
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.51
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.52
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.52
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.54
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.51
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.51
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.49
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.49
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.34
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.34
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.35
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.35
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.35
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.25
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.35
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.48
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.49
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.49
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.49
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.51
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.51
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.5
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.5
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.51
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.51
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.51
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.54
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.53
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.54
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.65
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.69
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.66
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.68
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.69
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.73
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.73
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.76
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.75
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.76
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.76
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.72
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.69
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.62
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.46
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.41
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.41
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.42
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.42
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.41
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.43
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.43
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.44
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.44
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.45
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.37
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.34
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.34
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.31
rpsA 1833979 c.438T>C synonymous_variant 0.12
rpsA 1833994 c.453G>T synonymous_variant 0.12
rpsA 1833997 c.456G>T synonymous_variant 0.12
rpsA 1834012 c.471G>A synonymous_variant 0.14
rpsA 1834015 c.474G>C synonymous_variant 0.14
rpsA 1834018 c.477C>T synonymous_variant 0.14
rpsA 1834024 c.483G>C synonymous_variant 0.14
rpsA 1834034 p.Ile165Val missense_variant 0.16
rpsA 1834039 c.498C>T synonymous_variant 0.17
rpsA 1834040 p.Lys167Gln missense_variant 0.17
rpsA 1834069 c.528G>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2153960 p.Pro718Ser missense_variant 1.0
PPE35 2167770 p.Ser948Ile missense_variant 0.99
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860213 p.Pro69Leu missense_variant 0.97
ribD 2987069 c.231T>C synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.88
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249012 c.2499G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0