TB-Profiler result

Run: SRR9971082
Summary

Run ID: SRR9971082

Sample name:

Date: 04-04-2023 23:10:10

Number of reads: 5071873

Percentage reads mapped: 93.5

Strain: lineage1.2.2.1

Drug-resistance: RR-TB

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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
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_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 491060 p.Met93Thr missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.37
ccsA 620659 p.Arg257Cys missense_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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778991 p.Val1Ala missense_variant 0.61
mmpR5 779099 c.110delG frameshift_variant 0.12
mmpR5 779254 p.Arg89Trp missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.99
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.13
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.11
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.1
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.12
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.21
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.24
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.24
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.23
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156004 c.108G>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser 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
kasA 2518306 c.192C>G synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
thyX 3068115 c.-170C>T upstream_gene_variant 1.0
thyA 3074034 c.438T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.2
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 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.18
embB 4247028 p.Leu172Arg missense_variant 0.24
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
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327450 c.-99G>A upstream_gene_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