TB-Profiler result

Run: SRR1172300
Summary

Run ID: SRR1172300

Sample name:

Date: 03-04-2023 03:03:15

Number of reads: 2796221

Percentage reads mapped: 91.39

Strain: lineage1.1.2

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
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
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
mshA 575703 p.Gly119Ala missense_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761349 p.Asp515Tyr missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.98
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpS5 778824 c.74_81delTGCAGCGG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.1
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.2
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.16
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.16
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.18
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.15
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.14
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.12
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.15
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.15
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.19
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.19
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.2
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.2
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.28
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.26
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.19
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.19
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.17
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476470 n.2813C>T 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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289751 c.-510C>T upstream_gene_variant 0.24
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859450 c.969C>T synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
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
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
embB 4247680 p.Met389Ile missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326432 p.Leu348Phe missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0