TB-Profiler result

Run: ERR9891979
Summary

Run ID: ERR9891979

Sample name:

Date: 02-04-2023 13:26:02

Number of reads: 651661

Percentage reads mapped: 99.42

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 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
katG 2155860 p.Met84Ile missense_variant 0.25 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 5084 c.-156G>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8967 p.Ala556Ser missense_variant 0.18
gyrA 9025 p.Arg575Leu missense_variant 0.18
gyrA 9323 c.2022C>A synonymous_variant 0.18
fgd1 490767 c.-16G>T upstream_gene_variant 0.15
mshA 575216 c.-132C>A upstream_gene_variant 0.18
mshA 576554 p.Asp403Tyr missense_variant 0.2
ccsA 619734 c.-157C>G upstream_gene_variant 0.17
ccsA 620562 c.672C>A synonymous_variant 0.14
rpoB 760789 p.Thr328Asn missense_variant 0.29
rpoB 761672 c.1866C>A synonymous_variant 0.17
rpoC 763841 p.Glu158Lys missense_variant 0.14
rpoC 763930 p.Glu187Asp missense_variant 0.19
rpoC 764355 p.Gln329Arg missense_variant 0.12
rpoC 766421 p.Gly1018Cys missense_variant 0.18
rpoC 766465 p.Gln1032His missense_variant 0.15
rpoC 766834 p.Glu1155Asp missense_variant 0.25
rpoC 766874 p.Asp1169Tyr missense_variant 0.25
rpoC 767210 p.Ala1281Ser missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777449 c.1032C>A synonymous_variant 0.2
mmpL5 777521 c.960C>A synonymous_variant 0.2
mmpL5 777554 c.927C>A synonymous_variant 0.18
mmpL5 777817 p.Val222Phe missense_variant 0.13
mmpL5 777917 c.564T>C synonymous_variant 0.13
mmpR5 778115 c.-875G>A upstream_gene_variant 0.14
mmpL5 778153 p.Asp110Tyr missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800639 c.-170C>A upstream_gene_variant 0.18
rplC 800668 c.-141C>A upstream_gene_variant 0.18
rplC 800673 c.-136G>T upstream_gene_variant 0.29
rplC 801426 c.618C>A synonymous_variant 0.21
fbiC 1305015 c.2085G>T synonymous_variant 0.44
Rv1258c 1406432 p.Met303Ile missense_variant 0.22
embR 1416778 c.570G>T synonymous_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
inhA 1674810 c.609C>A synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918079 p.Ser47Tyr missense_variant 0.17
tlyA 1918525 p.Gly196Trp missense_variant 0.22
tlyA 1918537 p.Asp200Tyr missense_variant 0.22
ndh 2102147 p.Arg299Leu missense_variant 0.18
ndh 2102193 c.850C>A synonymous_variant 0.2
ndh 2102391 p.Pro218Thr missense_variant 0.14
ndh 2102447 p.Gly199Val missense_variant 0.19
ndh 2102617 c.426C>T synonymous_variant 1.0
ndh 2103022 c.21C>A synonymous_variant 0.18
ndh 2103034 c.9C>A synonymous_variant 0.17
ndh 2103178 c.-137delC upstream_gene_variant 0.15
katG 2154247 p.Pro622His missense_variant 0.15
katG 2154807 c.1305C>A synonymous_variant 0.18
katG 2154926 p.Arg396Ser missense_variant 0.2
katG 2155022 p.Ile364Val missense_variant 0.11
katG 2155436 p.Gly226Trp missense_variant 0.15
katG 2155486 p.Arg209Leu missense_variant 0.13
katG 2155797 p.Met105Ile missense_variant 0.2
katG 2156342 c.-231G>T upstream_gene_variant 0.15
PPE35 2170016 c.597C>A synonymous_variant 0.17
PPE35 2170208 c.405C>A synonymous_variant 0.18
PPE35 2170225 p.Ala130Ser missense_variant 0.15
PPE35 2170229 c.384A>G synonymous_variant 0.15
PPE35 2170232 c.381T>A synonymous_variant 0.15
PPE35 2170401 p.Pro71Gln missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288684 c.558C>A synonymous_variant 0.14
pncA 2289011 c.231C>A synonymous_variant 0.17
pncA 2290212 c.-971G>T upstream_gene_variant 0.14
kasA 2518983 p.Ala290Glu missense_variant 0.22
kasA 2519009 p.Gly299Trp missense_variant 0.17
eis 2714813 p.Glu174* stop_gained 0.2
eis 2714879 p.Asp152Tyr missense_variant 0.2
eis 2714964 c.369C>A synonymous_variant 0.18
eis 2714967 p.Glu122Asp missense_variant 0.17
eis 2715055 p.Arg93Leu missense_variant 0.17
eis 2715361 c.-29G>T upstream_gene_variant 0.18
eis 2715445 c.-113C>A upstream_gene_variant 0.17
folC 2746136 c.1463G>T stop_lost&splice_region_variant 0.2
folC 2746171 c.1428G>C synonymous_variant 0.14
folC 2746387 c.1212C>A synonymous_variant 0.15
folC 2746390 c.1209G>T synonymous_variant 0.31
folC 2746561 c.1038C>A synonymous_variant 0.25
folC 2746776 p.Gln275Lys missense_variant 0.25
folC 2747098 c.501C>A synonymous_variant 0.18
folC 2747343 p.Val86Phe missense_variant 0.25
pepQ 2860263 c.156C>A synonymous_variant 0.2
Rv2752c 3065225 p.His323Asn missense_variant 0.13
Rv2752c 3065330 p.Asp288Tyr missense_variant 0.2
Rv2752c 3065426 p.Gly256Cys missense_variant 0.18
Rv2752c 3065567 p.Pro209Thr missense_variant 0.18
Rv2752c 3065572 p.Glu207Gly missense_variant 0.15
Rv2752c 3065646 c.546C>A synonymous_variant 0.18
Rv2752c 3067135 c.-944C>A upstream_gene_variant 0.12
thyX 3067952 c.-7G>T upstream_gene_variant 0.27
thyX 3068006 c.-62delG upstream_gene_variant 0.2
thyX 3068079 c.-134G>T upstream_gene_variant 0.2
ald 3086904 p.Arg29Ser missense_variant 0.19
ald 3087632 p.Gln271His missense_variant 0.27
ald 3087832 p.Ala338Glu missense_variant 0.14
Rv3083 3448437 c.-67C>A upstream_gene_variant 0.25
Rv3083 3448543 p.Leu14Ile missense_variant 0.17
fprA 3474471 p.Asn155Lys missense_variant 0.17
fprA 3474478 p.Val158Phe missense_variant 0.17
fprA 3475041 c.1035C>A synonymous_variant 0.17
fprA 3475216 p.Asp404Tyr missense_variant 0.24
Rv3236c 3611986 c.1131G>T synonymous_variant 0.18
Rv3236c 3612028 c.1089G>T synonymous_variant 0.2
Rv3236c 3612163 c.954G>T synonymous_variant 0.25
Rv3236c 3612169 p.Glu316Asp missense_variant 0.22
Rv3236c 3612208 c.909G>T synonymous_variant 0.22
Rv3236c 3612480 p.Pro213Thr missense_variant 0.17
Rv3236c 3612969 p.Gly50Trp missense_variant 0.2
Rv3236c 3613170 c.-54G>T upstream_gene_variant 0.15
fbiB 3641175 c.-360G>T upstream_gene_variant 0.17
fbiB 3641196 c.-339C>A upstream_gene_variant 0.2
fbiA 3641237 p.Ala232Glu missense_variant 0.2
fbiB 3641253 c.-282C>A upstream_gene_variant 0.17
fbiA 3641299 p.Arg253Ser missense_variant 0.17
fbiB 3641337 c.-198G>T upstream_gene_variant 0.18
fbiA 3641456 p.Ser305Leu missense_variant 0.22
fbiB 3641862 p.Gly110* stop_gained 0.18
fbiB 3642275 c.741A>G synonymous_variant 0.14
fbiB 3642411 c.877C>A synonymous_variant 0.17
fbiB 3642626 c.1092C>A synonymous_variant 0.18
alr 3840540 p.Ser294* stop_gained 0.19
rpoA 3878113 p.Gly132Val missense_variant 0.12
rpoA 3878550 c.-43C>A upstream_gene_variant 0.2
rpoA 3878635 c.-128C>A upstream_gene_variant 0.25
ddn 3987009 p.Thr56Ala missense_variant 0.11
clpC1 4038251 p.Phe818Leu missense_variant 0.21
clpC1 4038871 p.Glu612Gln missense_variant 0.12
clpC1 4038916 p.Ala597Ser missense_variant 0.17
panD 4044470 c.-189C>A upstream_gene_variant 0.27
embC 4239901 c.39G>T synonymous_variant 0.14
embC 4240027 c.165C>A synonymous_variant 0.22
embC 4240108 p.Leu82Phe missense_variant 0.18
embC 4240117 c.255C>A synonymous_variant 0.18
embC 4240217 p.Arg119Ser missense_variant 0.25
embC 4240312 c.450G>T synonymous_variant 0.25
embC 4240410 p.Pro183Gln missense_variant 0.22
embC 4240801 c.939C>T synonymous_variant 0.2
embC 4240803 p.Tyr314Phe missense_variant 0.2
embC 4241301 p.Ala480Asp missense_variant 0.17
embC 4241341 p.Phe493Leu missense_variant 0.22
embC 4241610 p.Pro583Gln missense_variant 0.18
embC 4241927 c.2065C>A synonymous_variant 0.17
embC 4242017 p.Glu719* stop_gained 0.21
embC 4242199 c.2337C>A synonymous_variant 0.2
embC 4242296 p.Asp812Tyr missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242838 c.-395C>A upstream_gene_variant 0.14
embA 4243355 c.123G>T synonymous_variant 0.18
embA 4243406 c.174C>A synonymous_variant 0.22
embA 4243948 p.Arg239Leu missense_variant 0.29
embA 4244032 p.Ile267Asn missense_variant 0.22
embA 4244085 p.Pro285Thr missense_variant 0.17
embA 4244297 c.1065G>A synonymous_variant 0.18
embA 4245555 p.Glu775* stop_gained 0.22
embB 4245674 c.-840A>T upstream_gene_variant 0.25
embA 4245718 p.Pro829Gln missense_variant 0.22
embA 4245767 p.Glu845Asp missense_variant 0.25
embB 4245830 c.-684G>T upstream_gene_variant 0.12
embB 4245905 c.-609C>A upstream_gene_variant 0.14
embB 4245959 c.-555G>A upstream_gene_variant 0.14
embB 4246816 c.303C>A synonymous_variant 0.25
embB 4247197 c.684C>A synonymous_variant 0.17
embB 4247689 c.1176G>T synonymous_variant 0.2
embB 4249283 p.Glu924* stop_gained 0.38
embB 4249299 p.Trp929Leu missense_variant 0.17
embB 4249367 p.Asp952Tyr missense_variant 0.18
embB 4249679 p.Asp1056Tyr missense_variant 0.29
embB 4249705 c.3192G>T synonymous_variant 0.25
embB 4249732 c.3219C>G synonymous_variant 1.0
aftB 4268140 p.Gly233* stop_gained 0.25
aftB 4268496 p.Arg114Leu missense_variant 0.17
ubiA 4269238 p.Ala199Val missense_variant 0.14
ethA 4327250 p.Ile75Asn missense_variant 0.14
ethA 4327266 p.Thr70Pro missense_variant 0.11
ethA 4327436 p.Gly13Val missense_variant 0.18
ethR 4327807 p.Leu87Ile missense_variant 0.17
ethR 4328086 p.Glu180* stop_gained 0.2
whiB6 4338289 p.Gly78Val missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0