TB-Profiler result

Run: SRR6896198
Summary

Run ID: SRR6896198

Sample name:

Date: 04-04-2023 17:58:32

Number of reads: 193656

Percentage reads mapped: 93.12

Strain: lineage2.2

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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 0.15 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
fgd1 491742 c.960T>C synonymous_variant 0.88
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576780 p.Val478Ala missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759651 c.-156A>G upstream_gene_variant 0.14
rpoB 760090 p.Gly95Glu missense_variant 0.2
rpoB 760375 p.Asp190Val missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766500 p.Ala1044Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305270 c.2340C>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417484 c.-137C>G upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472556 n.711C>A non_coding_transcript_exon_variant 0.2
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.2
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.2
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.15
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.29
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.29
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.25
rrl 1474280 n.623C>T non_coding_transcript_exon_variant 0.25
rrl 1474281 n.624A>G non_coding_transcript_exon_variant 0.25
rrl 1475635 n.1978G>T non_coding_transcript_exon_variant 0.25
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.31
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.42
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476433 n.2776C>T non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.2
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.17
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
fabG1 1673485 p.Arg16Cys missense_variant 0.18
fabG1 1674094 p.Gly219Arg missense_variant 0.22
rpsA 1833749 p.Ile70Leu missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.88
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714526 c.805_806delAC frameshift_variant 1.0
folC 2746441 p.Asp386Glu missense_variant 0.22
folC 2746544 p.Ala352Gly missense_variant 0.2
folC 2747784 c.-186C>T upstream_gene_variant 0.22
Rv2752c 3065137 p.Ile352Asn missense_variant 0.25
Rv2752c 3065711 p.Gly161Ser missense_variant 0.88
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449743 p.Ala414Ser missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475068 c.1062A>G synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641743 p.Arg70Lys missense_variant 0.25
rpoA 3877707 p.Glu267Asp missense_variant 0.22
clpC1 4040412 p.Leu98His missense_variant 0.2
panD 4044064 p.Gly73Val missense_variant 0.4
embC 4239994 c.132C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242703 c.-530C>A upstream_gene_variant 0.17
embA 4242772 c.-461G>A upstream_gene_variant 0.18
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244449 p.Ala406Asp missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268527 c.310C>A synonymous_variant 0.25
aftB 4268808 p.Val10Ala missense_variant 0.22
ubiA 4268963 p.Trp291Arg missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0