TB-Profiler result

Run: SRR6650411
Summary

Run ID: SRR6650411

Sample name:

Date: 04-04-2023 15:24:23

Number of reads: 2191131

Percentage reads mapped: 90.06

Strain: lineage1.1.3.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA RD239 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
gyrB 5117 c.-123G>A upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 0.92
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461187 p.Arg48Pro missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.12
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.12
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.11
rrs 1472139 n.294C>T non_coding_transcript_exon_variant 0.15
rrs 1472146 n.301G>A non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.17
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.17
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.18
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.18
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.15
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.19
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.17
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.18
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.19
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.2
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.2
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.24
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.23
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.23
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.26
rrs 1472733 n.888G>T non_coding_transcript_exon_variant 0.33
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.32
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.32
rrs 1472742 n.897C>A non_coding_transcript_exon_variant 0.32
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.31
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.32
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.32
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.26
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.21
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.3
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.35
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.35
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.38
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.47
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.52
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.38
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 0.97
tlyA 1917994 p.Ser19Pro missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074122 p.Asp117Gly missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612029 p.Ala363Val missense_variant 1.0
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407655 p.Ala183Glu missense_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0