TB-Profiler result

Run: SRR12882374
Summary

Run ID: SRR12882374

Sample name:

Date: 03-04-2023 07:31:29

Number of reads: 4501719

Percentage reads mapped: 84.22

Strain: lineage3.1.1

Drug-resistance: Sensitive

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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
lineage3.1.1 East-African-Indian CAS1-Kili 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
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 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
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 1472620 n.775A>G non_coding_transcript_exon_variant 0.12
rrs 1472634 n.789T>C non_coding_transcript_exon_variant 0.13
rrs 1472644 n.799C>G non_coding_transcript_exon_variant 0.14
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.29
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.29
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.29
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.1
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.21
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.29
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.3
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.3
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.3
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.3
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.3
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.3
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.3
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.3
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.31
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.21
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.18
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.13
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.19
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.21
rrl 1476246 n.2589G>A non_coding_transcript_exon_variant 0.3
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.29
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.3
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.31
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.38
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.34
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.34
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.33
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.33
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.34
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.38
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.37
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.39
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.46
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.47
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.51
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.47
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.46
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.45
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.42
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.42
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.34
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.3
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.26
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
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 2170461 p.Gly51Glu 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 4038845 c.1860G>T synonymous_variant 0.22
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249439 p.Glu976Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0