TB-Profiler result

Run: ERR2228903
Summary

Run ID: ERR2228903

Sample name:

Date: 31-03-2023 16:25:31

Number of reads: 318768

Percentage reads mapped: 99.15

Strain: lineage4

Drug-resistance: RR-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
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
rpoB 761136 p.Thr444Pro missense_variant 0.33 rifampicin
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 5429 p.Thr64Ser missense_variant 0.36
gyrB 5447 p.Leu70Phe missense_variant 0.22
gyrB 5757 p.Phe173Cys missense_variant 0.18
gyrB 6013 c.774G>T synonymous_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7666 p.Asp122Ala missense_variant 0.38
gyrA 7901 c.600G>T synonymous_variant 0.29
gyrA 8140 p.His280Leu missense_variant 0.4
gyrA 8148 p.Phe283Ile missense_variant 0.33
gyrA 8473 p.Leu391Gln missense_variant 0.33
mshA 576468 p.Val374Gly missense_variant 0.38
ccsA 619831 c.-60T>G upstream_gene_variant 0.67
ccsA 620160 c.270A>T synonymous_variant 0.29
rpoB 760168 p.Met121Lys missense_variant 0.33
rpoB 760309 p.Val168Glu missense_variant 0.5
rpoB 761869 p.Asp688Gly missense_variant 0.33
rpoB 763164 p.Lys1120* stop_gained 0.25
rpoB 763182 p.Cys1126Ser missense_variant 0.29
rpoC 764332 c.963G>A synonymous_variant 0.5
rpoC 765826 c.2457T>A synonymous_variant 0.33
rpoC 765941 p.Lys858* stop_gained 0.29
rpoC 767225 p.Pro1286Thr missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775677 p.Lys935Met missense_variant 0.25
mmpL5 776781 p.Leu567* stop_gained 0.4
mmpL5 777119 p.His454Gln missense_variant 0.38
mmpL5 777122 c.1359C>T synonymous_variant 0.43
mmpL5 777128 c.1353A>G synonymous_variant 0.38
mmpL5 777219 p.Leu421Gln missense_variant 0.57
mmpL5 777223 p.Tyr420Asn missense_variant 0.29
mmpL5 778325 p.Gln52His missense_variant 0.22
mmpR5 779054 p.Gln22Leu missense_variant 0.4
mmpL5 779100 c.-620A>C upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781535 c.-25A>G upstream_gene_variant 0.4
rplC 801293 p.Lys162Met missense_variant 0.22
fbiC 1303224 c.294C>T synonymous_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304581 p.Asn551Tyr missense_variant 0.33
Rv1258c 1406559 p.Gly261Asp missense_variant 0.5
embR 1416337 c.1011C>T synonymous_variant 0.33
atpE 1461075 p.Ile11Phe missense_variant 0.29
atpE 1461286 p.Lys81Met missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.5
rrs 1473255 n.1410A>T non_coding_transcript_exon_variant 0.25
rrs 1473362 n.1517C>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475812 n.2155T>A non_coding_transcript_exon_variant 0.5
rpsA 1833728 p.Ile63Leu missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102132 p.Gln304Leu missense_variant 0.4
ndh 2102184 p.Arg287Trp missense_variant 0.5
ndh 2102919 c.124C>T synonymous_variant 0.22
katG 2154373 p.Asp580Ala missense_variant 0.4
katG 2155298 p.Phe272Ile missense_variant 0.22
katG 2156177 c.-66T>A upstream_gene_variant 0.5
PPE35 2167813 c.2798_2799delAC frameshift_variant 0.29
PPE35 2167919 c.2694T>C synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 0.2
PPE35 2168657 c.1956T>A synonymous_variant 0.33
PPE35 2168665 p.Thr650Ser missense_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169476 c.1137C>A synonymous_variant 0.22
PPE35 2169751 p.Gly288* stop_gained 0.27
PPE35 2170035 p.Val193Gly missense_variant 0.2
Rv1979c 2222876 p.Thr97Pro missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289305 c.-64T>A upstream_gene_variant 0.25
pncA 2289306 c.-65A>T upstream_gene_variant 0.25
pncA 2290020 c.-779T>A upstream_gene_variant 0.43
kasA 2518695 p.Val194Gly missense_variant 0.22
kasA 2518823 p.Phe237Val missense_variant 0.25
eis 2715098 p.Thr79Pro missense_variant 0.67
eis 2715399 c.-67T>A upstream_gene_variant 0.22
ahpC 2726303 c.111T>A synonymous_variant 0.43
ahpC 2726521 p.Met110Lys missense_variant 0.5
ahpC 2726678 c.486G>A synonymous_variant 0.18
pepQ 2859730 p.His230Leu missense_variant 0.75
ribD 2986912 p.Asp25Ala missense_variant 0.67
ribD 2987417 p.Glu193Asp missense_variant 0.5
Rv2752c 3065645 p.Thr183Pro missense_variant 0.4
Rv2752c 3065732 p.Leu154Val missense_variant 0.33
Rv2752c 3066334 c.-143T>G upstream_gene_variant 0.33
thyX 3067839 p.Val36Gly missense_variant 0.3
ald 3086771 c.-49T>A upstream_gene_variant 0.4
ald 3086862 c.43C>A synonymous_variant 0.2
ald 3087161 c.342A>T synonymous_variant 0.4
fbiD 3339233 p.Val39Gly missense_variant 0.5
fbiD 3339431 p.Glu105Val missense_variant 0.5
fprA 3475370 p.Leu455Arg missense_variant 0.5
whiB7 3568561 p.Lys40Met missense_variant 0.33
Rv3236c 3612893 p.Leu75Gln missense_variant 0.29
Rv3236c 3612950 p.Glu56Val missense_variant 0.4
Rv3236c 3612962 p.Ala52Asp missense_variant 0.25
fbiA 3641240 p.Leu233Trp missense_variant 0.5
fbiB 3641959 p.Val142Gly missense_variant 0.22
fbiB 3642658 p.Val375Gly missense_variant 0.25
fbiB 3642677 c.1143A>C synonymous_variant 0.25
alr 3840758 p.Gln221His missense_variant 0.18
alr 3841423 c.-3T>G upstream_gene_variant 0.29
ddn 3987066 p.Val75Phe missense_variant 0.22
clpC1 4039069 p.Ser546Ala missense_variant 0.38
clpC1 4039443 p.Leu421Gln missense_variant 1.0
embC 4240489 c.627A>C synonymous_variant 0.43
embC 4242147 p.Asn762Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243276 p.Leu15Gln missense_variant 0.25
embA 4244427 p.Ser399Ala missense_variant 0.25
embA 4244772 p.Ser514Ala missense_variant 0.33
embA 4245457 p.Glu742Ala missense_variant 0.4
embA 4245541 p.Val770Gly missense_variant 1.0
embA 4245649 p.Ile806Thr missense_variant 0.67
embA 4245702 p.Ser824Ala missense_variant 1.0
embA 4245894 p.Tyr888Asn missense_variant 0.4
embB 4246814 p.Thr101Ala missense_variant 0.4
embB 4246911 p.Leu133* stop_gained 0.25
embB 4246917 p.Val135Glu missense_variant 0.33
embB 4249356 p.Val948Gly missense_variant 0.33
aftB 4268236 p.Leu201Val missense_variant 0.33
ethA 4327086 p.Thr130Pro missense_variant 0.5
ethR 4327841 p.Asp98Ala missense_variant 0.5
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338286 p.Val79Gly missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407863 p.Ile114Leu missense_variant 0.5
gid 4407924 c.279G>T synonymous_variant 0.33
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0