TB-Profiler result

Run: SRR12199431
Summary

Run ID: SRR12199431

Sample name:

Date: 03-04-2023 06:44:14

Number of reads: 6433047

Percentage reads mapped: 99.28

Strain: lineage4.3

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 0.79
lineage4.3 Euro-American (LAM) mainly-LAM None 0.89
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 0.21 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 0.99
rpoC 764995 c.1626C>G synonymous_variant 0.94
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 1472122 n.277G>A non_coding_transcript_exon_variant 0.13
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.13
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.13
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.13
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.15
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.15
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.18
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.16
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.15
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.14
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.14
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.14
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.13
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.14
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.1
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.11
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.11
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.16
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.21
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.23
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 0.17
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.17
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.19
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.21
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.27
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.22
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.22
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.23
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.17
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.17
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.17
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.19
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.16
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.18
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.16
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.17
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.16
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.17
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.2
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.27
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.34
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.35
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.31
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.32
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.31
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.29
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.32
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.27
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.21
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.2
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.2
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.19
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.19
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.2
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.2
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.2
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.2
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.2
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.2
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.24
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.22
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.22
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.13
fabG1 1673361 c.-79C>G upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.41
clpC1 4038287 c.2418C>T synonymous_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 0.17
aftB 4269606 c.-770T>C upstream_gene_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.96