TB-Profiler result

Run: SRR6831905
Summary

Run ID: SRR6831905

Sample name:

Date: 04-04-2023 17:06:31

Number of reads: 647953

Percentage reads mapped: 99.72

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 5214 c.-26C>G upstream_gene_variant 1.0
gyrB 6284 p.Asp349Tyr missense_variant 0.25
gyrA 6727 c.-575G>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8972 c.1671C>T synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576789 c.1442G>T stop_lost&splice_region_variant 0.18
ccsA 620371 c.485delC frameshift_variant 0.18
rpoC 763407 p.Gly13Asp missense_variant 0.4
rpoC 764434 p.Lys355Asn missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775887 p.Gly865Ala missense_variant 0.2
mmpL5 777595 p.Glu296Lys missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305482 p.Tyr851Ser missense_variant 0.22
Rv1258c 1406693 c.648G>T synonymous_variant 0.1
atpE 1461014 c.-31G>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473513 n.-145T>C upstream_gene_variant 0.14
rrl 1475362 n.1705G>T non_coding_transcript_exon_variant 0.13
rpsA 1833738 p.Arg66His missense_variant 0.12
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154807 c.1305C>A synonymous_variant 0.25
Rv1979c 2222015 p.Val384Ile missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2747651 c.-53C>T upstream_gene_variant 0.29
pepQ 2860199 p.Ala74Thr missense_variant 0.2
Rv2752c 3064692 p.Asp500Glu missense_variant 0.14
Rv2752c 3067135 c.-944C>T upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841421 c.-1A>G upstream_gene_variant 0.18
rpoA 3878427 p.Glu27Asp missense_variant 0.14
ddn 3987215 c.372A>G synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040858 c.-154G>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246227 c.2997delT frameshift_variant 0.15
embB 4248334 c.1821C>T synonymous_variant 0.2
embB 4248520 c.2007C>T synonymous_variant 0.12
aftB 4267280 c.1557G>A synonymous_variant 0.12
ethA 4326069 c.1405C>A synonymous_variant 0.29
ethR 4327673 p.Leu42Arg missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407720 c.483C>G synonymous_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0