TB-Profiler result

Run: ERR5866434
Summary

Run ID: ERR5866434

Sample name:

Date: 02-04-2023 00:41:09

Number of reads: 408330

Percentage reads mapped: 99.69

Strain: lineage4.8

Drug-resistance: MDR-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 0.98
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.18 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
gid 4407896 p.Glu103* stop_gained 0.93 streptomycin
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 5465 p.Glu76* stop_gained 0.27
gyrB 5722 c.483G>T synonymous_variant 0.3
gyrB 6159 c.923_925delTCA disruptive_inframe_deletion 0.2
gyrA 7189 c.-113C>A upstream_gene_variant 0.18
gyrA 7283 c.-19G>T upstream_gene_variant 0.2
gyrA 7307 c.6A>G synonymous_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7400 p.Met33Ile missense_variant 0.5
gyrA 7424 c.123G>T synonymous_variant 0.33
gyrA 7953 p.Ala218Ser missense_variant 0.15
gyrA 9091 p.Ala597Val missense_variant 0.18
gyrA 9248 c.1947G>T synonymous_variant 0.15
gyrA 9251 c.1950G>T synonymous_variant 0.15
gyrA 9608 p.Asp769Glu missense_variant 0.13
gyrA 9809 c.2508G>T synonymous_variant 0.18
fgd1 490589 c.-194G>T upstream_gene_variant 0.18
fgd1 490819 p.Glu13* stop_gained 0.29
fgd1 490936 p.Pro52Thr missense_variant 0.25
fgd1 491119 p.Glu113* stop_gained 0.18
fgd1 491307 c.525C>A synonymous_variant 0.15
fgd1 491322 c.540G>A synonymous_variant 0.17
fgd1 491723 p.Gly314Val missense_variant 0.22
mshA 575435 p.Pro30Thr missense_variant 0.15
mshA 575492 p.Leu49Met missense_variant 0.25
mshA 575954 p.Glu203* stop_gained 0.25
mshA 576248 p.Pro301Thr missense_variant 0.12
mshA 576382 c.1035G>T synonymous_variant 0.2
mshA 576419 p.Val358Phe missense_variant 0.22
mshA 576674 p.Arg443Ser missense_variant 0.25
ccsA 619720 c.-171C>A upstream_gene_variant 0.22
ccsA 619949 p.Ser20* stop_gained 0.33
ccsA 620045 p.Gly52Val missense_variant 0.25
ccsA 620095 p.His69Asn missense_variant 0.22
ccsA 620717 p.Ala276Val missense_variant 0.17
rpoB 761205 p.Arg467Ser missense_variant 0.15
rpoB 761533 p.Ser576* stop_gained 0.22
rpoB 761632 p.Ala609Glu missense_variant 0.18
rpoB 761730 p.Gly642Cys missense_variant 0.18
rpoB 761852 c.2046C>A synonymous_variant 0.4
rpoB 761939 p.Lys711Asn missense_variant 0.29
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoB 762275 c.2469C>A synonymous_variant 0.14
rpoC 762470 c.-900G>T upstream_gene_variant 0.4
rpoB 762559 p.Arg918Leu missense_variant 0.25
rpoB 762609 p.His935Tyr missense_variant 0.25
rpoC 763968 p.Gly200Val missense_variant 0.17
rpoC 764389 p.Leu340Phe missense_variant 0.4
rpoC 764665 c.1296C>A synonymous_variant 0.22
rpoC 764714 p.Leu449Met missense_variant 0.17
rpoC 765404 p.Leu679Met missense_variant 0.18
rpoC 765611 p.His748Asn missense_variant 0.15
rpoC 765813 p.Arg815Leu missense_variant 0.33
rpoC 767089 p.Cys1240* stop_gained 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775668 p.Trp938Leu missense_variant 0.18
mmpL5 775681 p.Gly934* stop_gained 0.15
mmpL5 775778 c.2703C>A synonymous_variant 0.15
mmpL5 775914 p.Ala856Asp missense_variant 0.25
mmpL5 776087 c.2394C>A synonymous_variant 0.5
mmpL5 777245 c.1236G>T synonymous_variant 0.25
mmpL5 777749 c.732C>T synonymous_variant 0.16
mmpR5 778445 c.-545G>T upstream_gene_variant 0.2
mmpS5 778613 p.Ser98Tyr missense_variant 0.27
mmpL5 779064 c.-584G>T upstream_gene_variant 0.17
mmpR5 779095 p.Ala36Ser missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781479 c.-81G>T upstream_gene_variant 0.19
rpsL 781745 p.Glu62Asp missense_variant 0.15
rpsL 781792 p.Ser78* stop_gained 0.18
rpsL 781813 p.Gly85Asp missense_variant 0.17
rplC 800771 c.-38C>A upstream_gene_variant 0.17
rplC 800976 p.Glu56Asp missense_variant 0.17
rplC 801186 c.378C>A synonymous_variant 0.17
fbiC 1302782 c.-149C>A upstream_gene_variant 0.25
fbiC 1302811 c.-120G>A upstream_gene_variant 0.15
fbiC 1302823 c.-108G>T upstream_gene_variant 0.15
fbiC 1302825 c.-106C>A upstream_gene_variant 0.15
fbiC 1302937 p.Gln3Lys missense_variant 0.2
fbiC 1304512 p.Val528Ile missense_variant 0.15
fbiC 1304682 c.1752C>A synonymous_variant 0.23
fbiC 1304722 p.Glu598* stop_gained 0.18
Rv1258c 1407057 p.Gly95Val missense_variant 0.15
Rv1258c 1407338 c.3G>T start_lost 0.4
Rv1258c 1407386 c.-46C>A upstream_gene_variant 0.4
embR 1417191 p.Asp53Tyr missense_variant 0.25
atpE 1461089 c.45G>T synonymous_variant 0.18
atpE 1461278 c.234A>G synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472562 n.717C>A non_coding_transcript_exon_variant 0.17
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.14
rrs 1473011 n.1166G>T non_coding_transcript_exon_variant 0.2
rrs 1473196 n.1351C>A non_coding_transcript_exon_variant 0.2
rrs 1473203 n.1358G>A non_coding_transcript_exon_variant 0.29
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474083 n.426C>A non_coding_transcript_exon_variant 0.43
rrl 1474262 n.605C>A non_coding_transcript_exon_variant 0.25
rrl 1474778 n.1121C>A non_coding_transcript_exon_variant 0.18
rrl 1474873 n.1217delA non_coding_transcript_exon_variant 0.22
rrl 1475596 n.1939G>T non_coding_transcript_exon_variant 0.17
rrl 1475690 n.2033G>T non_coding_transcript_exon_variant 0.15
rrl 1476513 n.2856G>A non_coding_transcript_exon_variant 0.15
rrl 1476725 n.3068C>A non_coding_transcript_exon_variant 0.22
rrl 1476756 n.3099G>T non_coding_transcript_exon_variant 0.17
fabG1 1673180 c.-260C>A upstream_gene_variant 0.2
fabG1 1673231 c.-209G>A upstream_gene_variant 0.18
fabG1 1673588 p.Gly50Glu missense_variant 0.22
fabG1 1673650 p.Ala71Ser missense_variant 0.17
fabG1 1674066 p.Lys209Asn missense_variant 0.22
inhA 1674328 c.127C>A synonymous_variant 0.29
inhA 1674507 c.306G>T synonymous_variant 0.4
inhA 1674637 p.Gly146Cys missense_variant 0.17
rpsA 1833504 c.-38_-37insC upstream_gene_variant 0.2
rpsA 1833539 c.-2_-1delAT upstream_gene_variant 0.18
rpsA 1834986 c.1445G>T stop_lost&splice_region_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918046 p.Gly36Val missense_variant 0.15
tlyA 1918182 c.243G>A synonymous_variant 0.22
tlyA 1918276 p.Val113Ile missense_variant 0.22
tlyA 1918378 p.Arg147Ser missense_variant 0.25
tlyA 1918495 p.Glu186* stop_gained 0.29
tlyA 1918548 p.Leu203Phe missense_variant 0.29
tlyA 1918703 p.Gly255Val missense_variant 0.33
ndh 2102152 c.891C>A synonymous_variant 0.18
ndh 2102732 p.Leu104Pro missense_variant 0.11
ndh 2103023 p.Pro7His missense_variant 0.18
katG 2154926 p.Arg396Ser missense_variant 0.33
katG 2155115 p.Leu333Ile missense_variant 0.25
katG 2155569 c.543C>T synonymous_variant 0.22
katG 2155659 c.453C>A synonymous_variant 0.25
katG 2155704 p.Pro136Ser missense_variant 0.2
katG 2155772 p.Arg114Ser missense_variant 0.25
katG 2156372 c.-261C>A upstream_gene_variant 0.2
katG 2156376 c.-265C>A upstream_gene_variant 0.22
PPE35 2167860 p.Gly918Val missense_variant 0.17
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168176 p.Gln813Lys missense_variant 0.3
PPE35 2168442 p.Trp724Leu missense_variant 0.15
PPE35 2170367 p.Gln82His missense_variant 0.2
PPE35 2170663 c.-51G>T upstream_gene_variant 0.17
Rv1979c 2222375 p.Gly264Cys missense_variant 0.2
Rv1979c 2222448 c.717G>T synonymous_variant 0.33
Rv1979c 2222499 c.666G>T synonymous_variant 0.17
Rv1979c 2222701 p.Gly155Val missense_variant 0.2
Rv1979c 2222837 p.Ala110Ser missense_variant 0.17
Rv1979c 2223259 c.-95C>A upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288822 c.420C>A synonymous_variant 0.15
pncA 2289175 p.Gly23Cys missense_variant 0.22
pncA 2289339 c.-98C>A upstream_gene_variant 0.18
pncA 2289549 c.-308G>T upstream_gene_variant 0.19
pncA 2289655 c.-414G>T upstream_gene_variant 0.29
kasA 2517936 c.-179G>T upstream_gene_variant 0.29
kasA 2518074 c.-41G>T upstream_gene_variant 0.22
kasA 2518101 c.-14G>T upstream_gene_variant 0.22
kasA 2518193 p.Pro27Ser missense_variant 0.22
kasA 2518216 p.Lys34Asn missense_variant 0.18
kasA 2518323 p.Ser70Ile missense_variant 0.18
kasA 2518329 c.218delG frameshift_variant 0.2
kasA 2518356 p.Ser81Leu missense_variant 0.17
kasA 2518513 c.399C>A synonymous_variant 0.15
kasA 2519069 p.Asp319Tyr missense_variant 0.25
ahpC 2726192 c.-1C>A upstream_gene_variant 0.19
folC 2746211 p.Arg463Ile missense_variant 0.2
folC 2746265 p.Ser445* stop_gained 0.25
folC 2746452 p.Gly383Cys missense_variant 0.15
folC 2746797 c.802C>A synonymous_variant 0.2
folC 2746918 c.681G>T synonymous_variant 0.2
folC 2747596 c.3G>T start_lost 0.22
folC 2747630 c.-32G>T upstream_gene_variant 0.18
pepQ 2859322 p.Pro366His missense_variant 0.15
pepQ 2859343 p.Pro359Gln missense_variant 0.17
pepQ 2859500 p.Gly307Cys missense_variant 0.29
pepQ 2859776 p.Gly215Cys missense_variant 0.25
pepQ 2860155 c.264C>A synonymous_variant 0.3
pepQ 2860166 p.Gly85Ser missense_variant 0.2
ribD 2986826 c.-13T>C upstream_gene_variant 0.14
ribD 2987032 p.Pro65His missense_variant 0.15
ribD 2987426 c.588G>T synonymous_variant 0.29
ribD 2987609 p.Lys257Asn missense_variant 0.22
Rv2752c 3064647 c.1545G>T synonymous_variant 0.15
Rv2752c 3066006 c.186G>T synonymous_variant 0.18
Rv2752c 3066102 p.Asn30Lys missense_variant 0.13
thyA 3074064 c.408C>A synonymous_variant 0.17
thyA 3074382 p.Phe30Leu missense_variant 0.22
thyA 3074394 c.78C>A synonymous_variant 0.2
ald 3086958 p.Asp47Asn missense_variant 0.17
ald 3087716 c.897G>T synonymous_variant 0.29
fbiD 3338979 c.-139G>T upstream_gene_variant 0.22
fbiD 3339305 p.Thr63Asn missense_variant 0.21
fbiD 3339310 p.Asp65Asn missense_variant 0.17
fbiD 3339317 p.Ala67Val missense_variant 0.17
fbiD 3339335 p.Ala73Val missense_variant 0.14
fbiD 3339580 p.Gly155Cys missense_variant 0.18
Rv3083 3448328 c.-176G>A upstream_gene_variant 0.5
fprA 3473862 c.-145C>A upstream_gene_variant 0.18
fprA 3473949 c.-58G>T upstream_gene_variant 0.4
fprA 3474193 p.Ile63Val missense_variant 0.2
fprA 3474218 p.Ala71Gly missense_variant 0.18
fprA 3474900 c.894C>A synonymous_variant 0.4
fprA 3475050 c.1044C>A synonymous_variant 0.25
fprA 3475104 c.1098G>A synonymous_variant 0.15
whiB7 3568729 c.-50G>T upstream_gene_variant 0.17
whiB7 3568778 c.-99C>A upstream_gene_variant 0.27
whiB7 3568810 c.-131G>A upstream_gene_variant 0.22
Rv3236c 3611982 p.Ala379Ser missense_variant 0.18
Rv3236c 3612421 c.696G>T synonymous_variant 0.18
Rv3236c 3613175 c.-59G>T upstream_gene_variant 0.2
Rv3236c 3613229 c.-113G>T upstream_gene_variant 0.17
fbiA 3640400 c.-143G>T upstream_gene_variant 0.2
fbiA 3640417 c.-126C>A upstream_gene_variant 0.14
fbiA 3641479 p.Pro313Thr missense_variant 0.22
fbiB 3641559 p.Ala9Ser missense_variant 0.18
fbiB 3641640 p.Ala36Ser missense_variant 0.2
fbiB 3642039 p.Gly169Cys missense_variant 0.25
fbiB 3642714 p.Gly394Cys missense_variant 0.17
alr 3840464 p.Phe319Leu missense_variant 0.17
rpoA 3878409 c.99C>A synonymous_variant 0.14
clpC1 4039729 p.Asp326Asn missense_variant 1.0
panD 4044057 c.225C>A synonymous_variant 0.22
panD 4044122 c.160C>A synonymous_variant 0.18
panD 4044174 c.108C>T synonymous_variant 0.22
panD 4044297 c.-16C>A upstream_gene_variant 0.18
panD 4044325 c.-44C>A upstream_gene_variant 0.2
embC 4239949 c.87C>T synonymous_variant 0.22
embC 4239989 p.Leu43Met missense_variant 0.18
embC 4240089 p.Gly76Val missense_variant 0.17
embC 4240465 p.Phe201Leu missense_variant 0.2
embC 4240485 p.Ala208Glu missense_variant 0.18
embC 4240506 p.Ser215* stop_gained 0.2
embC 4241054 p.Pro398Thr missense_variant 0.25
embC 4241069 p.Ala403Thr missense_variant 0.25
embC 4241388 p.Ser509Ile missense_variant 0.18
embC 4241431 p.Phe523Leu missense_variant 0.25
embC 4241455 c.1593C>A synonymous_variant 0.33
embC 4241490 p.Ala543Glu missense_variant 0.17
embC 4241777 p.Gly639Cys missense_variant 0.22
embC 4241808 p.Pro649Gln missense_variant 0.17
embA 4242313 c.-920C>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243410 c.182delC frameshift_variant 0.2
embA 4243574 c.342C>A synonymous_variant 0.29
embA 4243785 p.Leu185Met missense_variant 0.17
embA 4243808 p.Asp192Glu missense_variant 0.18
embA 4244859 p.Gly543Trp missense_variant 0.18
embA 4245508 p.Gly759Val missense_variant 0.33
embA 4245582 p.Asp784Tyr missense_variant 0.38
embA 4246047 p.Ala939Thr missense_variant 0.25
embA 4246279 p.Ala1016Val missense_variant 0.2
embA 4246396 p.Gly1055Val missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246849 p.Gln112His missense_variant 0.33
embB 4247005 c.492C>A synonymous_variant 0.22
embB 4247125 c.612G>T synonymous_variant 0.22
embB 4247632 c.1119C>A synonymous_variant 0.18
embB 4247890 c.1377C>A synonymous_variant 0.17
embB 4247999 p.Asp496Tyr missense_variant 0.18
embB 4248343 c.1830G>T synonymous_variant 0.18
embB 4249109 p.Pro866Thr missense_variant 0.15
aftB 4266978 p.Gly620Val missense_variant 0.2
aftB 4267183 p.Gly552Cys missense_variant 0.4
aftB 4267354 p.Gly495Cys missense_variant 0.2
aftB 4267586 c.1251C>A synonymous_variant 0.29
aftB 4267634 c.1203G>T synonymous_variant 0.22
aftB 4268254 p.Leu195Met missense_variant 0.18
aftB 4268903 c.-68delC upstream_gene_variant 0.25
aftB 4269012 c.-176G>T upstream_gene_variant 0.17
ubiA 4269484 p.Ala117Val missense_variant 0.15
ubiA 4269648 p.Phe62Leu missense_variant 0.22
aftB 4269804 c.-968G>T upstream_gene_variant 0.15
ethA 4326224 p.Val417Ala missense_variant 0.1
ethA 4326326 p.Thr383Met missense_variant 0.15
ethA 4326418 c.1056G>T synonymous_variant 0.18
ethA 4326483 p.Arg331Ser missense_variant 0.22
ethA 4326657 p.Pro273Ser missense_variant 0.2
ethA 4326897 p.Ala193Ser missense_variant 0.22
ethA 4327216 p.Lys86Asn missense_variant 0.17
ethR 4327228 c.-321G>T upstream_gene_variant 0.2
ethA 4327257 p.Gln73Lys missense_variant 0.2
ethR 4327882 p.Glu112Gln missense_variant 0.13
gid 4407698 p.Asp169Tyr missense_variant 0.27
gid 4407786 c.417G>T synonymous_variant 0.15
gid 4408372 c.-170G>C upstream_gene_variant 0.2
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0