TB-Profiler result

Run: ERR2229163
Summary

Run ID: ERR2229163

Sample name:

Date: 31-03-2023 16:45:59

Number of reads: 337703

Percentage reads mapped: 99.33

Strain: lineage4

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
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 6265 c.1026C>T synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9809 c.2508G>T synonymous_variant 0.4
gyrA 9813 p.Asn838Asp missense_variant 0.4
fgd1 491356 p.Phe192Leu missense_variant 0.18
mshA 575166 c.-182G>A upstream_gene_variant 0.38
rpoB 761953 p.Ala716Val missense_variant 0.33
rpoC 765413 p.Pro682Thr missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776417 c.2064G>A synonymous_variant 0.5
mmpL5 777119 p.His454Gln missense_variant 0.33
mmpL5 777122 c.1359C>T synonymous_variant 0.4
mmpL5 777128 c.1353A>G synonymous_variant 0.4
mmpL5 777160 p.Ala441Ser missense_variant 0.22
mmpL5 777204 p.Pro426Leu missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304875 p.Ile649Val missense_variant 0.33
fbiC 1305338 p.Gly803Val missense_variant 0.33
Rv1258c 1406879 c.462T>C synonymous_variant 0.14
atpE 1461082 p.Gly13Val missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471926 n.81C>G non_coding_transcript_exon_variant 0.2
rrl 1473731 n.74T>C non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153966 p.Ala716Ser missense_variant 0.15
katG 2155469 p.Asp215Tyr missense_variant 0.33
katG 2156342 c.-231G>T upstream_gene_variant 0.15
katG 2156534 c.-423G>A upstream_gene_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.25
PPE35 2167967 c.2646A>C synonymous_variant 0.25
PPE35 2167999 p.Pro872Ala missense_variant 0.4
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2222121 c.1044G>T synonymous_variant 0.22
Rv1979c 2222395 p.Pro257Leu missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289387 c.-146C>A upstream_gene_variant 0.2
pncA 2290071 c.-831delT upstream_gene_variant 0.67
eis 2714340 c.993C>T synonymous_variant 0.17
Rv2752c 3064801 p.Glu464Val missense_variant 0.33
Rv3083 3448386 c.-118C>A upstream_gene_variant 0.33
alr 3841093 c.328C>T synonymous_variant 0.4
rpoA 3877732 p.Arg259Leu missense_variant 0.18
rpoA 3878481 c.27G>T synonymous_variant 0.5
clpC1 4039508 c.1197G>C synonymous_variant 0.33
embC 4241229 p.Leu456Pro missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245292 p.Ser687Phe missense_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.18
ethR 4326964 c.-585G>A upstream_gene_variant 0.2
ethR 4326970 c.-579G>T upstream_gene_variant 0.25
ethA 4327160 p.Ile105Thr missense_variant 0.33
ethR 4327589 p.Gly14Asp missense_variant 0.22
ethA 4328340 c.-867A>G upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408001 p.Ile68Phe missense_variant 0.18
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0