TB-Profiler result

Run: ERR1750942
Summary

Run ID: ERR1750942

Sample name:

Date: 31-03-2023 15:00:53

Number of reads: 1300841

Percentage reads mapped: 97.09

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 0.99
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 5605 c.366C>T synonymous_variant 1.0
gyrB 6138 p.Ser300* stop_gained 0.25
gyrA 7270 c.-32C>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7947 p.Leu216Met missense_variant 0.12
gyrA 8040 p.Gly247Ser missense_variant 0.15
gyrA 8094 p.Gly265Cys missense_variant 0.18
gyrA 8195 c.894C>A synonymous_variant 0.4
fgd1 491066 p.Cys95Phe missense_variant 0.13
mshA 576508 c.1161C>A synonymous_variant 0.14
ccsA 620748 c.858T>G synonymous_variant 0.38
rpoB 760221 p.Gly139Ser missense_variant 0.2
rpoB 760865 c.1059C>A synonymous_variant 0.18
rpoB 761586 p.Asp594Asn missense_variant 0.14
rpoB 762256 p.Ala817Val missense_variant 0.2
rpoB 762523 p.Pro906Gln missense_variant 0.17
rpoB 763125 p.Pro1107Ser missense_variant 0.17
rpoB 763313 p.Glu1169Asp missense_variant 0.2
rpoC 764743 c.1374G>A synonymous_variant 0.12
rpoC 766846 c.3477C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778220 c.-770G>A upstream_gene_variant 0.4
mmpS5 779572 c.-667G>T upstream_gene_variant 0.22
mmpS5 779644 c.-739G>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304984 c.2055_2056delGC frameshift_variant 0.14
embR 1416514 c.834T>C synonymous_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
rrl 1474517 n.860C>A non_coding_transcript_exon_variant 0.5
rpsA 1834473 p.Val311Ala missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154316 p.Gly599Glu missense_variant 0.25
katG 2155124 p.Asn330Tyr missense_variant 0.22
PPE35 2167859 c.2754T>G synonymous_variant 0.27
PPE35 2167982 c.2631C>T synonymous_variant 0.2
PPE35 2168013 c.2599delG frameshift_variant 0.29
PPE35 2168034 p.Thr860Ile missense_variant 0.29
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168221 p.Ala798Thr missense_variant 0.4
PPE35 2168249 c.2364G>A synonymous_variant 0.25
PPE35 2169149 c.1464G>C synonymous_variant 1.0
PPE35 2169410 c.1203C>T synonymous_variant 0.15
Rv1979c 2222238 p.Leu309Asn missense_variant 0.17
Rv1979c 2222263 p.Arg301Gln missense_variant 0.17
Rv1979c 2223277 c.-113C>T upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.25
kasA 2518151 p.Ser13Arg missense_variant 0.22
eis 2714569 p.Ala255Gly missense_variant 0.36
eis 2715211 p.Pro41His missense_variant 0.15
ahpC 2726338 p.Val49Gly missense_variant 0.33
ahpC 2726341 p.Val50Gly missense_variant 0.5
Rv2752c 3064781 p.Gly471Ser missense_variant 0.18
ald 3087673 p.His285Pro missense_variant 0.33
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3475159 p.Asn385Tyr missense_variant 0.14
fprA 3475167 c.1161C>T synonymous_variant 0.13
Rv3236c 3612085 c.1032C>A synonymous_variant 0.15
Rv3236c 3612968 p.Gly50Val missense_variant 0.17
fbiA 3641255 p.Ala238Val missense_variant 0.17
ddn 3987083 c.240C>A synonymous_variant 0.2
clpC1 4038495 p.Arg737Leu missense_variant 0.22
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039867 p.Gly280Ser missense_variant 0.14
clpC1 4039877 c.828C>A synonymous_variant 0.15
clpC1 4040687 c.18C>T synonymous_variant 0.18
panD 4044167 c.115C>T synonymous_variant 0.15
embC 4240190 p.Pro110Ser missense_variant 0.15
embC 4240822 c.960C>T synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243349 c.117C>A synonymous_variant 0.2
embA 4245557 p.Glu775Asp missense_variant 0.22
embB 4249795 c.3282C>A synonymous_variant 0.4
aftB 4267019 c.1816_1817delCC frameshift_variant 0.14
aftB 4267194 p.Pro548Gln missense_variant 1.0
ubiA 4270009 c.-176C>T upstream_gene_variant 1.0
ethA 4326905 p.Leu190Pro missense_variant 0.24
ethA 4327297 p.Met59Ile missense_variant 0.4
ethR 4327704 p.Lys52Asn missense_variant 0.17
ethA 4328358 c.-885C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0