TB-Profiler result

Run: SRR6046528
Summary

Run ID: SRR6046528

Sample name:

Date: 04-04-2023 12:18:25

Number of reads: 1441450

Percentage reads mapped: 58.1

Strain: lineage3.1.2.1

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
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 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 0.71 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
gyrA 9793 p.Asn831Ser missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 576622 c.1275C>T synonymous_variant 0.11
rpoB 759615 c.-192A>C upstream_gene_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762083 c.2277T>C synonymous_variant 0.1
rpoB 762086 c.2280G>C synonymous_variant 0.11
rpoB 762101 c.2295C>G synonymous_variant 0.1
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
mmpS5 778835 p.Thr24Met missense_variant 1.0
mmpS5 778941 c.-36A>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.4
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.4
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.4
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.71
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.71
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.71
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.89
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.89
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.89
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.89
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.89
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.9
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.4
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.89
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.89
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.89
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.8
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 0.75
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.8
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.67
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.8
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.75
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.83
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.83
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.71
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.71
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.71
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.71
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.5
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.75
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.75
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.75
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.75
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.75
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.75
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.75
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.75
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.75
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.75
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.75
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.8
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.8
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.88
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.89
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.69
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.77
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 0.15
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.8
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.8
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.75
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.44
rrl 1476638 n.2981C>A non_coding_transcript_exon_variant 0.2
rpsA 1833716 p.Thr59Ala missense_variant 1.0
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 2168604 p.Pro670Leu 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 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039652 c.1053G>T synonymous_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248629 p.Pro706Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0