TB-Profiler result

Run: ERR2228831
Summary

Run ID: ERR2228831

Sample name:

Date: 31-03-2023 16:22:18

Number of reads: 390774

Percentage reads mapped: 99.34

Strain: lineage4.8

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
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
rpoB 761004 p.Thr400Ala missense_variant 0.4 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 5056 c.-184A>T upstream_gene_variant 0.5
gyrB 5302 p.Glu21Asp missense_variant 0.5
gyrB 6356 p.Thr373Ser missense_variant 0.5
gyrA 7346 c.45C>T synonymous_variant 0.2
gyrA 7349 p.Glu16Asp missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7549 p.Asn83Ile missense_variant 0.18
gyrA 9157 p.Asp619Ala missense_variant 0.4
gyrA 9757 p.Ala819Asp missense_variant 0.2
fgd1 490892 p.Val37Gly missense_variant 0.5
fgd1 491769 c.987A>C synonymous_variant 0.43
mshA 575260 c.-88A>C upstream_gene_variant 0.2
mshA 575617 c.270C>T synonymous_variant 0.22
mshA 575900 p.Asn185Asp missense_variant 0.15
mshA 576468 p.Val374Gly missense_variant 0.3
ccsA 619964 p.Leu25Arg missense_variant 0.25
ccsA 620132 p.Leu81Arg missense_variant 0.25
ccsA 620380 p.Met164Leu missense_variant 0.25
ccsA 620533 p.Met215Leu missense_variant 0.4
ccsA 620713 p.Tyr275Asp missense_variant 0.25
rpoB 760740 p.Lys312* stop_gained 0.5
rpoB 760887 p.Thr361Pro missense_variant 0.27
rpoB 760900 p.Asp365Ala missense_variant 0.33
rpoB 761044 p.Asn413Ile missense_variant 0.33
rpoB 762766 p.Leu987Arg missense_variant 0.4
rpoC 762854 c.-516G>A upstream_gene_variant 0.14
rpoB 763036 p.Tyr1077Cys missense_variant 0.22
rpoC 763974 p.Glu202Ala missense_variant 0.27
rpoC 765085 c.1716T>G synonymous_variant 0.29
rpoC 765615 p.Tyr749Phe missense_variant 0.33
rpoC 765713 p.Thr782Ser missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777113 p.Met456Ile missense_variant 0.22
mmpL5 777166 p.Ser439Thr missense_variant 0.25
mmpL5 777479 p.Thr334Pro missense_variant 0.29
mmpL5 778954 c.-474T>C upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781396 c.-164T>G upstream_gene_variant 0.22
fbiC 1303295 p.Tyr122Phe missense_variant 0.29
fbiC 1303553 p.Ala208Glu missense_variant 0.4
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303831 p.Thr301Ala missense_variant 0.22
fbiC 1303997 p.Gly356Asp missense_variant 0.22
fbiC 1304210 p.Asp427Ala missense_variant 0.22
fbiC 1304805 c.1875G>A synonymous_variant 0.33
fbiC 1305030 c.2100G>T synonymous_variant 0.4
fbiC 1305413 p.Lys828Met missense_variant 0.18
fbiC 1305415 p.Thr829Pro missense_variant 0.27
Rv1258c 1406226 p.Asp372Ala missense_variant 0.38
Rv1258c 1406551 p.Leu264Val missense_variant 0.33
embR 1416826 p.His174Gln missense_variant 0.2
embR 1417277 p.Asp24Ala missense_variant 1.0
atpE 1460948 c.-97A>T upstream_gene_variant 0.67
atpE 1460970 c.-75A>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472903 n.1058A>T non_coding_transcript_exon_variant 0.22
rrl 1473418 n.-240G>C upstream_gene_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.4
rrl 1475744 n.2087A>T non_coding_transcript_exon_variant 0.5
fabG1 1673159 c.-281T>G upstream_gene_variant 0.5
rpsA 1833359 c.-183T>G upstream_gene_variant 0.4
rpsA 1833517 c.-25A>T upstream_gene_variant 0.43
rpsA 1833541 c.-1T>A upstream_gene_variant 0.29
rpsA 1833543 c.2T>A start_lost 0.29
rpsA 1834320 p.Val260Gly missense_variant 0.29
rpsA 1834609 c.1068T>G synonymous_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918607 p.Val223Gly missense_variant 0.33
katG 2154622 p.Ile497Thr missense_variant 0.4
katG 2156297 c.-186T>G upstream_gene_variant 0.75
katG 2156391 c.-280T>G upstream_gene_variant 0.4
PPE35 2168114 c.2499T>A synonymous_variant 0.4
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.5
PPE35 2169219 p.Leu465Gln missense_variant 0.5
PPE35 2169725 p.Asn296Lys missense_variant 0.33
PPE35 2169748 p.Ile289Phe missense_variant 0.33
PPE35 2169884 c.729T>A synonymous_variant 0.25
PPE35 2170227 p.Asn129Ile missense_variant 0.5
PPE35 2170351 p.Thr88Ala missense_variant 0.4
PPE35 2170746 c.-134A>T upstream_gene_variant 0.18
Rv1979c 2221878 c.1287A>T synonymous_variant 1.0
Rv1979c 2222101 p.Ile355Asn missense_variant 0.4
Rv1979c 2222596 p.Val190Glu missense_variant 0.5
Rv1979c 2222786 p.Trp127Gly missense_variant 0.22
Rv1979c 2223064 p.Leu34Gln missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288862 p.Glu127Val missense_variant 0.33
pncA 2289405 c.-164A>T upstream_gene_variant 0.33
kasA 2518199 p.Ile29Val missense_variant 0.5
kasA 2518663 c.549T>G synonymous_variant 0.27
kasA 2518898 p.Leu262Val missense_variant 0.15
eis 2714283 p.Glu350Asp missense_variant 0.29
eis 2714515 p.Asp273Ala missense_variant 0.5
eis 2715168 c.165T>G synonymous_variant 0.33
folC 2746331 p.Glu423Ala missense_variant 0.2
folC 2746711 p.Glu296Asp missense_variant 0.43
folC 2746865 p.Leu245Arg missense_variant 0.5
folC 2747211 p.Leu130Val missense_variant 0.29
ribD 2987239 p.Thr134Asn missense_variant 0.29
Rv2752c 3064552 p.Arg547Leu missense_variant 0.67
Rv2752c 3065314 c.875_877delCCG disruptive_inframe_deletion 0.5
Rv2752c 3066313 c.-122T>G upstream_gene_variant 0.29
Rv2752c 3066350 c.-159T>G upstream_gene_variant 0.33
Rv2752c 3067162 c.-971T>C upstream_gene_variant 0.33
thyX 3067383 p.Asn188Thr missense_variant 0.43
thyA 3074515 c.-44T>G upstream_gene_variant 0.33
thyA 3074627 c.-156T>A upstream_gene_variant 0.4
ald 3086997 p.Thr60Ser missense_variant 0.22
ald 3087190 p.Asp124Ala missense_variant 0.38
ald 3087307 p.Val163Gly missense_variant 0.25
ald 3087316 p.Val166Gly missense_variant 0.25
ald 3087744 p.Ser309Ala missense_variant 0.33
fprA 3474238 p.Phe78Ile missense_variant 0.33
fprA 3474967 p.Ser321Thr missense_variant 0.4
Rv3236c 3612195 p.Thr308Ser missense_variant 0.25
Rv3236c 3612340 c.777A>G synonymous_variant 0.33
Rv3236c 3613029 p.Leu30Val missense_variant 0.43
fbiA 3641059 p.Trp173Gly missense_variant 0.38
fbiA 3641279 p.Ile246Ser missense_variant 0.25
fbiB 3641340 c.-195T>C upstream_gene_variant 0.33
fbiB 3641953 p.Leu140Arg missense_variant 0.29
fbiB 3641959 p.Val142Gly missense_variant 0.25
fbiB 3642332 p.Phe266Leu missense_variant 0.25
fbiB 3642385 p.Leu284Arg missense_variant 0.22
alr 3841612 c.-193_-192insC upstream_gene_variant 0.33
rpoA 3877540 p.Tyr323Phe missense_variant 0.33
ddn 3987079 p.Lys79Arg missense_variant 0.12
ddn 3987275 p.Ile144Met missense_variant 0.13
clpC1 4039104 p.Arg534Leu missense_variant 0.22
clpC1 4039830 p.Leu292* stop_gained 0.67
clpC1 4040144 c.561G>C synonymous_variant 0.25
clpC1 4040249 p.Glu152Asp missense_variant 0.29
embC 4239837 c.-26A>G upstream_gene_variant 0.22
embC 4240023 p.Gln54Arg missense_variant 0.4
embC 4241043 p.Asn394Thr missense_variant 0.25
embC 4241450 p.Ser530Ala missense_variant 0.36
embC 4242146 p.Asn762Tyr missense_variant 0.22
embC 4242151 c.2289A>T synonymous_variant 0.22
embC 4242305 p.Ile815Leu missense_variant 0.2
embC 4242566 p.Thr902Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244118 p.Tyr296His missense_variant 0.33
embA 4245342 p.Ser704Ala missense_variant 0.25
embA 4245657 p.Ser809Thr missense_variant 0.33
embB 4246220 c.-294T>C upstream_gene_variant 0.22
embB 4246226 c.-288C>T upstream_gene_variant 0.22
embB 4246265 c.-249C>T upstream_gene_variant 0.33
embB 4247777 p.Ser422Ala missense_variant 0.19
embB 4247920 c.1407T>A synonymous_variant 0.4
embB 4249659 p.Met1049Lys missense_variant 0.29
aftB 4267473 p.Gly455Val missense_variant 0.25
aftB 4267572 p.His422Pro missense_variant 0.22
ubiA 4269388 p.Glu149Val missense_variant 0.29
ethR 4326961 c.-588G>C upstream_gene_variant 0.18
ethR 4326964 c.-585G>A upstream_gene_variant 0.18
ethR 4326970 c.-579G>T upstream_gene_variant 0.2
ethR 4327288 c.-261T>A upstream_gene_variant 0.5
whiB6 4338280 p.Ile81Asn missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408430 c.-228G>T upstream_gene_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0