TB-Profiler result

Run: SRR6044963
Summary

Run ID: SRR6044963

Sample name:

Date: 04-04-2023 11:50:23

Number of reads: 1729890

Percentage reads mapped: 90.73

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 0.33 streptomycin
pncA 2288817 p.Thr142Met missense_variant 1.0 pyrazinamide
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
fgd1 490994 p.Gly71Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576488 p.Val381His missense_variant 0.17
mshA 576751 p.Lys468Asn missense_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile 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 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.5
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.33
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.33
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.5
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.6
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.6
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.6
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.6
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.6
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.6
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.7
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 1472616 n.771G>A non_coding_transcript_exon_variant 0.4
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.4
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.33
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.4
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.33
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.43
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.43
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.4
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.12
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.33
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.38
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.38
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.3
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.3
rrl 1475883 n.2226A>G non_coding_transcript_exon_variant 0.29
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.21
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.19
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.18
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.28
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.22
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.19
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.25
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.25
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.27
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.15
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.27
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.21
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.21
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.2
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.22
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.32
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.35
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.29
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.35
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.38
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.38
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168812 p.Thr601Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fbiD 3339341 p.Leu75Arg missense_variant 0.12
fbiD 3339564 c.447G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642703 p.Val390Ala missense_variant 0.11
alr 3841473 c.-53G>A upstream_gene_variant 0.99
ddn 3987095 c.252G>A synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242402 p.Arg847His missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0