TB-Profiler result

Run: SRR6855681
Summary

Run ID: SRR6855681

Sample name:

Date: 04-04-2023 17:42:07

Number of reads: 780422

Percentage reads mapped: 99.11

Strain: lineage4.8.1;lineage3.1.1

Drug-resistance: Other

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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 0.07
lineage4 Euro-American LAM;T;S;X;H None 0.94
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.86
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.06
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.89
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.15 streptomycin
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
mshA 576470 p.Gly375Ser missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.93
fabG1 1673436 c.-3delG upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.29
PPE35 2168149 p.Pro822Ser missense_variant 0.95
PPE35 2170391 c.222G>T synonymous_variant 0.11
PPE35 2170461 p.Gly51Glu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288895 c.338_346delGCACGCCAC disruptive_inframe_deletion 0.5
ald 3086788 c.-32T>C upstream_gene_variant 0.17
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.24
fbiB 3642874 p.Leu447Arg missense_variant 0.79
embC 4240172 p.Val104Met missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244781 p.Arg517Ser missense_variant 0.11
embA 4244784 c.1552C>A synonymous_variant 0.11
embA 4245918 c.2690delG frameshift_variant 0.11
embB 4249744 c.3231G>A synonymous_variant 0.25
embB 4249751 c.3238T>C synonymous_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0