TB-Profiler result

Run: SRR21677863

Summary

Run ID: SRR21677863

Sample name:

Date: 04-04-2023 02:48:51

Number of reads: 764594

Percentage reads mapped: 99.22

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491304 c.522C>T synonymous_variant 0.12
fgd1 491538 c.756G>C synonymous_variant 0.12
ccsA 619734 c.-157C>A upstream_gene_variant 0.2
rpoC 766169 p.Gly934Ser missense_variant 0.12
rpoC 766616 p.Arg1083Gly missense_variant 0.11
rpoC 767016 p.Ala1216Asp missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407046 p.Asp99His missense_variant 0.12
Rv1258c 1407413 c.-74delG upstream_gene_variant 0.11
embR 1416187 c.1161C>A synonymous_variant 0.11
atpE 1460907 c.-138T>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 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154084 c.2028G>T synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168863 c.1750C>T synonymous_variant 0.1
PPE35 2170107 p.Ala169Asp missense_variant 0.33
PPE35 2170411 p.Ala68Ser missense_variant 0.12
Rv1979c 2222373 c.792C>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289807 c.-566G>T upstream_gene_variant 0.13
kasA 2519065 c.951C>A synonymous_variant 0.11
kasA 2519213 p.Ile367Phe missense_variant 0.14
eis 2715418 c.-86T>C upstream_gene_variant 0.11
ribD 2986934 p.Tyr32* stop_gained 0.11
Rv2752c 3064612 p.Ile527Thr missense_variant 0.1
Rv2752c 3064806 c.1386G>T synonymous_variant 0.12
Rv2752c 3064828 c.1361_1363delCCG disruptive_inframe_deletion 0.15
thyX 3067290 p.Leu219Pro missense_variant 0.11
thyA 3074659 c.-188G>T upstream_gene_variant 0.12
ald 3087557 c.738A>G synonymous_variant 1.0
fbiD 3339597 c.480G>T synonymous_variant 0.14
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474198 p.Ser64Arg missense_variant 0.11
fprA 3474374 c.369dupC frameshift_variant 0.11
fbiB 3642313 p.Arg260Leu missense_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040093 c.612C>T synonymous_variant 1.0
clpC1 4040140 p.Pro189Thr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243837 p.Leu202Pro missense_variant 0.1
embA 4245406 p.Ala725Gly missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.19
embB 4246556 p.Ala15Pro missense_variant 0.19
embB 4246563 p.Leu17Trp missense_variant 0.17
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4246849 p.Gln112His missense_variant 0.12
aftB 4267406 p.Lys477Asn missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338700 c.-179T>G upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0