TB-Profiler result

Run: SRR6896236
Summary

Run ID: SRR6896236

Sample name:

Date: 04-04-2023 17:59:41

Number of reads: 245816

Percentage reads mapped: 99.79

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 5666 p.Gly143Arg missense_variant 1.0
gyrA 7318 p.Leu6Ser missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 763532 p.Thr55Ala missense_variant 0.17
rpoC 765105 p.Leu579Pro missense_variant 0.14
rpoC 766373 p.Ser1002Pro missense_variant 0.25
rpoC 767103 p.Leu1245Pro missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776721 c.1754_1759delTCTACT disruptive_inframe_deletion 0.14
mmpL5 777079 p.Ile468Val missense_variant 0.33
mmpL5 777672 p.Ala270Val missense_variant 0.11
mmpL5 778789 c.-309G>C upstream_gene_variant 0.18
rpsL 781364 c.-196A>C upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303428 c.498C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474911 n.1254G>A non_coding_transcript_exon_variant 0.12
rrl 1474974 n.1317G>C non_coding_transcript_exon_variant 0.14
rrl 1475830 n.2176dupA non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918107 c.168C>A synonymous_variant 0.29
ndh 2101660 c.1383G>C synonymous_variant 0.14
ndh 2103152 c.-110G>A upstream_gene_variant 0.14
katG 2155458 c.654C>T synonymous_variant 0.2
PPE35 2169414 p.Gly400Val missense_variant 0.13
PPE35 2170251 p.Val121Gly missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518285 c.171G>C synonymous_variant 0.12
kasA 2518389 p.Gly92Glu missense_variant 0.12
eis 2714264 p.Gly357Ser missense_variant 0.2
folC 2746628 p.Asp324Val missense_variant 0.2
folC 2746701 p.His300Tyr missense_variant 0.17
folC 2747218 p.Ile127Met missense_variant 0.2
pepQ 2859581 p.Leu280Val missense_variant 0.29
fbiD 3339039 c.-78delT upstream_gene_variant 0.12
fbiB 3642767 p.Glu411Asp missense_variant 0.12
alr 3840764 c.657G>C synonymous_variant 1.0
alr 3841433 c.-13G>T upstream_gene_variant 0.14
rpoA 3877858 p.Glu217Val missense_variant 0.15
ddn 3987033 p.Leu64Phe missense_variant 0.11
clpC1 4039789 p.Ser306Thr missense_variant 0.12
embC 4240860 p.Leu333Pro missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244073 p.Ala281Pro missense_variant 0.17
embB 4247678 c.1166delT frameshift_variant 0.4
aftB 4267610 c.1227C>T synonymous_variant 0.33
ubiA 4269803 p.Ala11Thr missense_variant 0.11
ethA 4328067 c.-594T>C upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407633 c.570A>G synonymous_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0