TB-Profiler result

Run: SRR6896157
Summary

Run ID: SRR6896157

Sample name:

Date: 04-04-2023 17:57:14

Number of reads: 574583

Percentage reads mapped: 99.63

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
mshA 575687 p.Ala114Ser missense_variant 0.12
mshA 576118 c.771C>A synonymous_variant 0.12
rpoB 761631 p.Ala609Ser missense_variant 0.12
rpoC 767001 p.Thr1211Met missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778617 p.Pro97Thr missense_variant 0.12
mmpR5 779125 p.Cys46Arg missense_variant 0.13
mmpL5 779175 c.-695G>A upstream_gene_variant 0.12
mmpR5 779182 p.Gly65Trp missense_variant 0.12
mmpR5 779192 p.Ser68Ile missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303170 c.240C>A synonymous_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 0.12
fbiC 1304716 p.Ala596Ser missense_variant 0.14
Rv1258c 1407268 p.Val25Ile missense_variant 0.12
atpE 1460875 c.-170C>A upstream_gene_variant 0.13
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
tlyA 1918301 p.Ser121Leu missense_variant 1.0
ndh 2103008 p.Pro12His missense_variant 0.17
ndh 2103054 c.-12G>T upstream_gene_variant 0.17
katG 2153997 c.2115G>T synonymous_variant 0.17
katG 2155257 c.855C>A synonymous_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168841 p.Val591Ala missense_variant 0.11
PPE35 2169674 c.939T>C synonymous_variant 0.12
Rv1979c 2223203 c.-39G>T upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223301 c.-137C>T upstream_gene_variant 0.12
kasA 2518089 c.-25delA upstream_gene_variant 0.12
eis 2715016 p.Arg106Leu missense_variant 0.12
eis 2715578 c.-246C>T upstream_gene_variant 0.2
folC 2746159 c.1440C>A synonymous_variant 0.17
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3475045 c.1039C>A synonymous_variant 0.12
rpoA 3878305 p.Gly68Val missense_variant 0.17
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4241435 p.Ala525Ser missense_variant 0.14
embC 4242275 p.Asp805Tyr missense_variant 0.14
embC 4242297 p.Asp812Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249726 c.3213C>A synonymous_variant 0.14
ethR 4327994 p.Thr149Met missense_variant 0.12
whiB6 4338590 c.-69A>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0