TB-Profiler result

Run: ERR4815944
Summary

Run ID: ERR4815944

Sample name:

Date: 01-04-2023 14:09:07

Number of reads: 391753

Percentage reads mapped: 84.9

Strain: lineage4.1.2.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 2155650 c.461delA frameshift_variant 0.29 isoniazid
embB 4247586 p.Gly358Val missense_variant 0.14 ethambutol
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 5415 p.Ala59Val missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7901 c.600G>A synonymous_variant 0.33
gyrA 9283 p.Gly661Asp missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490694 c.-89G>C upstream_gene_variant 0.4
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620814 c.924C>T synonymous_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760197 p.Ala131Thr missense_variant 0.22
rpoB 760872 p.Glu356* stop_gained 0.33
rpoB 761767 p.Val654Gly missense_variant 0.25
rpoB 762200 c.2394C>T synonymous_variant 0.2
rpoB 762212 c.2406G>C synonymous_variant 0.25
rpoB 762218 c.2412T>C synonymous_variant 0.36
rpoB 762233 c.2427G>C synonymous_variant 0.33
rpoB 762234 p.Pro810Ser missense_variant 0.33
rpoB 762239 c.2433G>A synonymous_variant 0.31
rpoB 762245 c.2439G>C synonymous_variant 0.31
rpoB 762254 c.2448T>C synonymous_variant 0.27
rpoB 762293 c.2487T>C synonymous_variant 0.25
rpoC 763528 c.159G>T synonymous_variant 0.25
rpoC 763531 c.162G>C synonymous_variant 0.22
rpoC 763534 c.165T>C synonymous_variant 0.22
rpoC 763537 c.168C>G synonymous_variant 0.22
rpoC 763546 c.177A>G synonymous_variant 0.22
rpoC 763570 c.201G>T synonymous_variant 0.29
rpoC 763594 c.225C>T synonymous_variant 0.22
rpoC 763603 c.234C>T synonymous_variant 0.22
rpoC 763609 c.240C>T synonymous_variant 0.29
rpoC 763619 p.Arg84Lys missense_variant 0.2
rpoC 763622 p.Ala85Ser missense_variant 0.22
rpoC 763642 c.273G>T synonymous_variant 0.25
rpoC 763654 c.285C>T synonymous_variant 0.29
rpoC 763660 c.291T>G synonymous_variant 0.33
rpoC 763669 c.300C>G synonymous_variant 0.33
rpoC 763675 c.306C>G synonymous_variant 0.33
rpoC 764404 c.1035C>T synonymous_variant 0.25
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.25
rpoC 764424 p.Asn352Thr missense_variant 0.15
rpoC 764428 c.1059G>A synonymous_variant 0.17
rpoC 764431 c.1062G>C synonymous_variant 0.15
rpoC 764434 c.1065A>G synonymous_variant 0.23
rpoC 764435 c.1066_1068delAGGinsCGT synonymous_variant 0.31
rpoC 764441 p.Ile358Leu missense_variant 0.23
rpoC 764446 p.Asp359Glu missense_variant 0.13
rpoC 764458 c.1089G>C synonymous_variant 0.24
rpoC 764461 c.1092A>G synonymous_variant 0.24
rpoC 764485 c.1116G>C synonymous_variant 0.13
rpoC 764497 c.1128A>G synonymous_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.15
rpoC 764548 c.1179G>C synonymous_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766167 p.Ala933Val missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776143 p.Gly780Arg missense_variant 0.17
mmpL5 776516 c.1964delT frameshift_variant 0.15
mmpL5 777648 p.Ala278Val missense_variant 0.15
mmpS5 778768 c.136_137delGA frameshift_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781485 c.-75C>A upstream_gene_variant 0.12
Rv1258c 1406089 p.Ala418Thr missense_variant 0.18
atpE 1461196 p.Thr51Lys missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.6
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.8
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.33
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.91
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.62
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.73
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.69
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.9
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.8
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.38
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.64
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.79
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.4
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.79
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.4
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.4
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.5
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.5
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.67
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.67
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 1.0
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 1.0
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.67
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 1.0
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 1.0
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 1.0
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.29
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.67
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.67
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.88
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.9
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.9
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.83
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.67
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.83
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.83
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.83
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.83
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.5
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.33
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.83
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.83
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.83
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.64
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 0.75
rrs 1473122 n.1278A>T non_coding_transcript_exon_variant 0.88
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.95
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.94
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.91
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.8
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 1.0
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.86
rrs 1473291 n.1446G>C non_coding_transcript_exon_variant 0.33
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.4
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.5
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.6
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.57
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.71
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.83
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.83
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.83
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.83
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.8
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.88
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.89
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.88
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 0.86
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.89
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.33
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.67
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.67
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.67
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.67
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.67
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.67
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.83
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.75
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.67
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.67
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.67
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.67
fabG1 1673322 c.-118C>G upstream_gene_variant 0.4
rpsA 1834249 c.708T>C synonymous_variant 1.0
rpsA 1834261 c.720A>G synonymous_variant 1.0
rpsA 1834264 c.723G>C synonymous_variant 1.0
rpsA 1834294 c.753G>C synonymous_variant 0.5
rpsA 1834298 p.Gln253Glu missense_variant 0.5
rpsA 1834306 c.765T>C synonymous_variant 0.4
rpsA 1834307 p.Asp256Gln missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155403 p.Gly237Ser missense_variant 0.22
katG 2156396 c.-285C>T upstream_gene_variant 0.22
PPE35 2170226 c.386delA frameshift_variant 1.0
Rv1979c 2222394 c.771G>T synonymous_variant 0.17
Rv1979c 2222443 p.Ala241Asp missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290114 c.-873T>C upstream_gene_variant 0.33
pncA 2290225 c.-987_-985delGTT upstream_gene_variant 0.67
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518840 c.726C>T synonymous_variant 0.18
pepQ 2859401 p.Asp340Asn missense_variant 0.12
thyX 3067199 c.747A>G synonymous_variant 0.15
thyA 3073790 p.Pro228Thr missense_variant 0.14
thyA 3073821 c.651G>A synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448537 p.Ala12Pro missense_variant 0.33
Rv3083 3449250 c.747C>T synonymous_variant 0.17
Rv3083 3449700 c.1197C>A synonymous_variant 0.15
Rv3083 3449739 p.His412Gln missense_variant 0.14
Rv3083 3449792 p.Ala430Val missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475131 c.1125C>A synonymous_variant 0.29
fprA 3475202 p.Pro399Gln missense_variant 0.2
Rv3236c 3612097 c.1020C>T synonymous_variant 0.22
Rv3236c 3613001 p.Ala39Val missense_variant 0.25
fbiB 3642746 c.1212C>A synonymous_variant 0.18
rpoA 3878132 p.Ala126Ser missense_variant 0.2
clpC1 4039018 p.Ser563Ala missense_variant 0.2
clpC1 4039022 c.1683A>G synonymous_variant 0.22
clpC1 4039042 p.Ser555Thr missense_variant 0.15
clpC1 4040624 c.80delA frameshift_variant 0.25
clpC1 4040753 c.-49G>T upstream_gene_variant 0.2
embC 4240045 p.Trp61* stop_gained 0.22
embC 4240875 p.Ser338Asn missense_variant 0.22
embC 4242307 c.2446delA frameshift_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242941 p.His1027Asp missense_variant 0.25
embA 4244693 c.1463delA frameshift_variant 0.22
embA 4245272 c.2040G>A synonymous_variant 0.11
embB 4247071 c.562delG frameshift_variant 0.18
embB 4247263 c.757_759delCTC conservative_inframe_deletion 0.2
embB 4249015 c.2502C>T synonymous_variant 0.17
ethA 4326504 p.Gly324Arg missense_variant 0.67
ethR 4327702 p.Lys52Gln missense_variant 0.5
ethA 4328251 c.-780_-779delCT upstream_gene_variant 0.14
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0