TB-Profiler result

Run: SRR5341356
Summary

Run ID: SRR5341356

Sample name:

Date: 04-04-2023 10:16:58

Number of reads: 4023476

Percentage reads mapped: 91.62

Strain: lineage3

Drug-resistance: MDR-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
lineage3 East-African-Indian CAS 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288827 p.Val139Met missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 1.0
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
fbiC 1305366 p.Met812Ile missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471926 n.81C>T non_coding_transcript_exon_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.14
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.14
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.15
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.12
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.12
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.11
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.12
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.21
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.2
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.22
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.13
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.15
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.11
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.22
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.2
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.32
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.31
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.26
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918172 p.Ala78Val missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156008 p.Asn35Thr missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.19
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
kasA 2519092 p.Ile326Met missense_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568857 c.-178C>T upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 1.0
panD 4044023 c.259C>T synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248103 c.1590G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407871 c.331delG frameshift_variant 1.0