TB-Profiler result

Run: SRR5818666

Summary

Run ID: SRR5818666

Sample name:

Date: 04-04-2023 11:41:39

Number of reads: 378082

Percentage reads mapped: 80.88

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 0.31 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
gyrB 5846 p.Gly203Trp missense_variant 0.2
gyrB 6458 p.Val407Leu 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
gyrA 9596 c.2295G>T synonymous_variant 0.89
fgd1 490801 p.Gly7Ser missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761191 p.Ala462Val missense_variant 0.14
rpoB 762148 p.Arg781Gln missense_variant 0.12
rpoB 762162 p.Ile786Phe missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778664 p.Ile81Asn missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303574 p.Leu215Pro missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471712 n.-134T>C upstream_gene_variant 0.18
rrs 1472258 n.413A>T non_coding_transcript_exon_variant 0.15
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.22
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.18
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.18
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.18
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.18
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.18
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.17
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.17
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.18
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.18
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.18
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.18
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.18
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.18
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.31
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.31
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.31
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.29
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.27
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.27
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.23
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.25
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.25
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.25
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.29
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.29
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.21
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.22
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.17
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.17
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.18
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.18
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.18
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.17
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.17
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.17
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.18
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.29
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.23
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.25
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.31
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.24
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.33
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.21
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.21
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.21
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.21
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.21
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.21
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.21
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.27
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.29
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.48
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.46
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.48
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.42
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.41
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.45
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.26
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.18
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.12
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.12
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12
rrl 1476720 n.3063G>T non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102751 p.Cys98Gly missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168351 c.2262T>C synonymous_variant 0.29
PPE35 2168931 p.Pro561Leu missense_variant 0.11
PPE35 2169031 p.Asp528Tyr missense_variant 0.22
PPE35 2169091 p.Val508Leu missense_variant 0.25
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
thyX 3067441 p.Gln169* stop_gained 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448560 c.57G>T synonymous_variant 0.17
Rv3083 3449066 c.565delG frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613009 c.108T>C synonymous_variant 0.14
fbiB 3641487 c.-48G>A upstream_gene_variant 0.12
fbiB 3641614 p.Asp27Val missense_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244721 p.Gln497Lys missense_variant 0.29
embB 4247028 p.Leu172Arg missense_variant 0.5
embB 4249370 c.2857C>T synonymous_variant 0.14
aftB 4268619 p.Val73Gly missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0