TB-Profiler result

Run: ERR2229647
Summary

Run ID: ERR2229647

Sample name:

Date: 31-03-2023 17:23:16

Number of reads: 427022

Percentage reads mapped: 99.08

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2154205 p.Ala636Glu missense_variant 0.12 isoniazid
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 5467 p.Glu76Asp missense_variant 0.18
gyrB 6505 p.Lys422Asn missense_variant 0.15
gyrA 6667 c.-635G>A upstream_gene_variant 0.33
gyrB 6726 p.Val496Glu missense_variant 0.33
gyrA 6874 c.-428G>A upstream_gene_variant 0.22
gyrA 7309 p.Asp3Gly missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8046 p.Gly249Ser missense_variant 0.2
gyrA 9746 c.2445C>T synonymous_variant 0.25
fgd1 490896 p.Ser38Arg missense_variant 0.17
mshA 575891 p.Ala182Thr missense_variant 0.5
mshA 576036 p.Ala230Asp missense_variant 0.18
rpoB 760045 p.Leu80Pro missense_variant 0.17
rpoB 760487 c.681G>A synonymous_variant 0.33
rpoB 760631 c.825G>A synonymous_variant 0.17
rpoB 760713 c.910delC frameshift_variant 0.22
rpoB 762210 p.Pro802Thr missense_variant 0.25
rpoC 764620 c.1251G>T synonymous_variant 0.22
rpoC 766729 p.Glu1120Asp missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778524 p.Ala128Ser missense_variant 0.4
mmpL5 779010 c.-530G>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800637 c.-172G>A upstream_gene_variant 0.17
fbiC 1303742 p.Ala271Asp missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304551 p.Gly541Cys missense_variant 0.15
fbiC 1305486 c.2556C>A synonymous_variant 0.12
fbiC 1305498 c.2568C>A synonymous_variant 0.18
Rv1258c 1406903 p.Tyr146* stop_gained 0.4
embR 1416452 p.Arg299Leu missense_variant 0.18
embR 1417109 p.Arg80His missense_variant 0.22
atpE 1461172 p.Pro43His missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472846 n.1001C>A non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.22
rrs 1473156 n.1311A>G non_coding_transcript_exon_variant 0.17
rrl 1473898 n.241C>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474815 n.1158A>C non_coding_transcript_exon_variant 0.25
rrl 1475081 n.1424C>G non_coding_transcript_exon_variant 0.29
rrl 1475091 n.1434G>T non_coding_transcript_exon_variant 0.25
rrl 1475652 n.1995C>A non_coding_transcript_exon_variant 0.2
fabG1 1673229 c.-211C>A upstream_gene_variant 0.18
inhA 1674069 c.-133G>T upstream_gene_variant 0.67
inhA 1674518 c.320dupC frameshift_variant 0.29
inhA 1674633 c.432C>T synonymous_variant 0.2
rpsA 1834648 c.1107C>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917980 p.Arg14Leu missense_variant 0.22
tlyA 1918534 p.His199Asn missense_variant 0.22
ndh 2101985 p.Gly353Val missense_variant 0.25
ndh 2102783 p.Gly87Asp missense_variant 0.12
katG 2154217 p.Arg632Leu missense_variant 0.13
PPE35 2167746 p.Thr956Ser missense_variant 0.15
PPE35 2167814 c.2799C>T synonymous_variant 0.22
PPE35 2168040 p.Ala858Gly missense_variant 0.15
PPE35 2168043 p.Ala857Gly missense_variant 0.17
PPE35 2168047 p.Leu856Val missense_variant 0.33
PPE35 2168051 p.Val854Ile missense_variant 0.17
PPE35 2168247 p.Leu789Pro missense_variant 0.4
PPE35 2168419 p.Asp732Tyr missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.14
PPE35 2169293 c.1320T>C synonymous_variant 0.15
PPE35 2169341 c.1272A>C synonymous_variant 0.13
PPE35 2169348 p.Phe422Ser missense_variant 0.13
PPE35 2169357 p.Thr419Ile missense_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.64
PPE35 2170053 p.Thr187Ser missense_variant 0.64
PPE35 2170576 p.Ala13Ser missense_variant 0.14
Rv1979c 2221807 p.Val453Ala missense_variant 0.12
Rv1979c 2222419 p.Asp249Val missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289492 c.-251C>T upstream_gene_variant 1.0
kasA 2518611 p.Thr166Asn missense_variant 0.5
kasA 2518823 p.Phe237Val missense_variant 0.25
kasA 2518987 p.Met291Ile missense_variant 0.25
pepQ 2860009 p.Ala137Asp missense_variant 0.2
ribD 2987493 p.Val219Phe missense_variant 0.25
ribD 2987505 p.Leu223Met missense_variant 0.25
Rv2752c 3064680 c.1512C>T synonymous_variant 0.17
Rv2752c 3065026 p.Arg389Leu missense_variant 0.15
Rv2752c 3065809 p.Val128Asp missense_variant 0.5
thyX 3067990 c.-45C>A upstream_gene_variant 0.22
thyA 3074523 c.-52G>T upstream_gene_variant 0.29
ald 3087603 p.Ala262Ser missense_variant 0.18
fbiD 3339324 c.207G>T synonymous_variant 0.2
Rv3083 3448417 c.-87C>A upstream_gene_variant 0.25
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474316 p.Val104Phe missense_variant 0.5
fprA 3474751 p.Ile249Phe missense_variant 0.12
fbiB 3642044 c.510G>T synonymous_variant 0.17
alr 3840835 p.His196Asn missense_variant 0.25
alr 3840886 p.Leu179Ile missense_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 0.29
ddn 3986663 c.-181G>A upstream_gene_variant 0.25
clpC1 4038746 c.1959C>A synonymous_variant 0.17
clpC1 4040575 p.Val44Phe missense_variant 0.13
clpC1 4040903 c.-199C>A upstream_gene_variant 0.15
panD 4044321 c.-40A>G upstream_gene_variant 0.25
embC 4240142 p.Leu94Met missense_variant 0.25
embC 4240858 c.996G>A synonymous_variant 0.4
embC 4241692 c.1830C>A synonymous_variant 0.4
embC 4242113 c.2251C>T synonymous_variant 0.5
embC 4242221 p.Pro787Thr missense_variant 0.33
embA 4242355 c.-878A>T upstream_gene_variant 0.18
embC 4242603 p.Ser914* stop_gained 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243026 p.Arg1055Met missense_variant 0.18
embA 4244602 p.Ala457Val missense_variant 0.17
embA 4245820 p.Ser863Asn missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4247937 p.Thr475Met missense_variant 0.29
embB 4248276 p.Thr588Lys missense_variant 0.18
embB 4249383 p.Pro957Gln missense_variant 0.22
aftB 4268171 c.666G>A synonymous_variant 0.2
aftB 4268255 c.582G>T synonymous_variant 0.13
aftB 4268366 p.Cys157* stop_gained 0.22
ubiA 4269918 c.-85G>T upstream_gene_variant 0.15
ubiA 4269955 c.-122T>A upstream_gene_variant 0.15
ethA 4326631 p.His281Gln missense_variant 0.13
ethA 4326712 p.Gln254His missense_variant 0.13
ethA 4326791 p.Trp228Leu missense_variant 0.15
ethR 4327312 c.-237G>T upstream_gene_variant 0.25
ethA 4327319 p.Gly52Ala missense_variant 0.2
ethR 4327321 c.-228G>T upstream_gene_variant 0.2
ethA 4327478 c.-5G>T upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407790 p.Ala138Glu missense_variant 0.18
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0