TB-Profiler result

Run: ERR4797427
Summary

Run ID: ERR4797427

Sample name:

Date: 01-04-2023 07:38:58

Number of reads: 2825660

Percentage reads mapped: 99.81

Strain: lineage4.8;lineage3

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
lineage3 East-African-Indian CAS RD750 0.15
lineage4 Euro-American LAM;T;S;X;H None 0.83
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.85
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.17
mshA 575424 p.Arg26His missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576111 p.Ala255Gly missense_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.37
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474413 n.756A>C non_coding_transcript_exon_variant 0.29
rrl 1475737 n.2080G>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 0.76
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 0.24
Rv3083 3449922 c.1419G>T synonymous_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.2
fbiB 3642877 p.Lys448Arg missense_variant 0.23
rpoA 3878641 c.-134C>G upstream_gene_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 0.81
embC 4242075 p.Arg738Gln missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268619 p.Val73Gly missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.21