TB-Profiler result

Run: ERR4819075
Summary

Run ID: ERR4819075

Sample name:

Date: 01-04-2023 15:54:35

Number of reads: 510351

Percentage reads mapped: 94.16

Strain: lineage4.1.2.1

Drug-resistance: Other

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 Euro-American T;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 0.99
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
tlyA 1918116 c.181_182dupGC frameshift_variant 0.14 capreomycin
tlyA 1918517 c.582delC frameshift_variant 0.17 capreomycin
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 5458 c.221dupG frameshift_variant 0.22
gyrB 5855 p.Ile206Val missense_variant 0.17
gyrB 6561 p.Lys441Arg missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7802 c.501C>T synonymous_variant 0.15
gyrA 8150 p.Phe283Leu missense_variant 0.12
gyrA 8814 p.Val505Ile missense_variant 0.22
gyrA 9295 c.1996delT frameshift_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9327 p.Ala676Pro missense_variant 0.15
gyrA 9682 p.Ala794Val missense_variant 0.22
fgd1 491371 p.Gly197Ser missense_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576374 p.Ala343Thr missense_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761232 p.Arg476Trp missense_variant 0.14
rpoB 761363 p.Ser519Arg missense_variant 0.14
rpoB 762142 c.2337delT frameshift_variant 0.15
rpoC 764134 c.765C>G synonymous_variant 0.17
rpoC 764376 p.Ala336Val missense_variant 0.17
rpoC 764925 c.1557delC frameshift_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766681 p.His1104Gln missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775758 p.Thr908Ile missense_variant 0.25
mmpL5 776341 p.His714Tyr missense_variant 0.11
mmpL5 776984 p.Phe499Leu missense_variant 0.2
mmpL5 778339 p.Val48Ile missense_variant 0.22
mmpS5 778490 p.Val139Glu missense_variant 0.2
mmpL5 778825 c.-345G>A upstream_gene_variant 0.12
mmpR5 779113 p.Trp42Arg missense_variant 0.17
mmpR5 779122 p.Val45Leu missense_variant 0.12
mmpR5 779285 c.299delT frameshift_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302832 c.-99G>A upstream_gene_variant 0.11
fbiC 1303075 c.147delC frameshift_variant 0.14
fbiC 1305440 p.Ala837Val missense_variant 0.11
Rv1258c 1406859 p.Gly161Asp missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.4
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.33
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.33
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.33
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.33
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.33
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.5
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.5
rrs 1473017 n.1172A>G non_coding_transcript_exon_variant 0.5
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.5
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.5
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.5
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.5
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.5
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.5
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.4
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.4
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.4
rrl 1473384 n.-274A>G upstream_gene_variant 0.67
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.43
inhA 1674981 c.780C>A synonymous_variant 0.13
rpsA 1833754 p.Lys71Asn missense_variant 0.11
tlyA 1917939 c.-1C>T upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918419 p.Leu160Phe missense_variant 0.29
ndh 2101853 p.Leu397Pro missense_variant 0.25
ndh 2101962 p.Pro361Ser missense_variant 0.18
ndh 2102888 c.154delC frameshift_variant 0.15
ndh 2103129 c.-88delC upstream_gene_variant 0.2
katG 2154200 p.Tyr638His missense_variant 0.12
katG 2155521 c.591T>C synonymous_variant 0.29
PPE35 2167886 c.2727C>T synonymous_variant 0.2
PPE35 2168282 c.2331C>T synonymous_variant 0.29
PPE35 2170355 c.258G>C synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288815 p.Ala143Ser missense_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518114 c.-1A>T upstream_gene_variant 0.12
eis 2714288 p.Ile349Val missense_variant 0.17
eis 2714447 c.885delG frameshift_variant 0.12
eis 2714691 c.642G>A synonymous_variant 0.2
eis 2714738 p.Glu199* stop_gained 0.18
eis 2715292 p.Pro14Leu missense_variant 0.17
folC 2747346 p.Leu85Met missense_variant 0.12
ribD 2986750 c.-88delC upstream_gene_variant 0.15
ribD 2986842 p.Pro2Ser missense_variant 0.12
ribD 2987044 p.Phe69Ser missense_variant 0.11
Rv2752c 3064538 p.Val552Leu missense_variant 0.22
Rv2752c 3064755 c.1437C>G synonymous_variant 0.11
Rv2752c 3064797 c.1395G>A synonymous_variant 0.17
Rv2752c 3064844 p.Asp450Asn missense_variant 0.13
Rv2752c 3066030 c.159_161delCGA disruptive_inframe_deletion 0.14
thyX 3067449 p.Gln166Arg missense_variant 0.17
thyA 3074192 p.Tyr94His missense_variant 0.2
thyA 3074350 p.Gly41Asp missense_variant 0.12
thyA 3074532 c.-61C>A upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086996 c.177C>T synonymous_variant 0.12
ald 3087005 p.Asp62Glu missense_variant 0.11
ald 3087019 p.Asp67Val missense_variant 0.12
fbiD 3339439 p.Ser108Pro missense_variant 0.17
Rv3083 3449046 c.543C>T synonymous_variant 0.17
Rv3083 3449299 p.Arg266Trp missense_variant 0.12
fprA 3473882 c.-125A>G upstream_gene_variant 0.12
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
fprA 3474070 p.Leu22Met missense_variant 0.17
fprA 3475024 p.Thr340Ala missense_variant 0.25
Rv3236c 3612701 p.Asp139Val missense_variant 0.13
fbiB 3641073 c.-462T>G upstream_gene_variant 0.13
fbiB 3642312 p.Arg260Cys missense_variant 0.14
alr 3840454 p.Gly323Ser missense_variant 0.12
alr 3840878 c.543A>G synonymous_variant 0.11
embC 4240481 p.Pro207Ser missense_variant 0.17
embC 4240822 c.960C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242695 p.Leu945Met missense_variant 0.17
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244108 p.Asn292Lys missense_variant 0.12
embA 4244986 p.Gly585Val missense_variant 0.17
embA 4245035 c.1803C>T synonymous_variant 0.18
embB 4247450 p.Ala313Thr missense_variant 0.14
embB 4249115 p.Pro868Ser missense_variant 0.12
embB 4249143 p.Val877Ala missense_variant 0.12
aftB 4266965 c.1871delC frameshift_variant 0.22
aftB 4267449 p.Val463Glu missense_variant 0.1
aftB 4268247 p.Leu197Arg missense_variant 0.12
aftB 4268262 p.Ile192Thr missense_variant 0.12
ubiA 4269251 p.Glu195* stop_gained 0.12
ubiA 4269278 p.Phe186Leu missense_variant 0.11
ubiA 4269767 p.Pro23Thr missense_variant 0.17
ubiA 4269904 c.-71G>A upstream_gene_variant 0.22
ethA 4327314 p.Arg54Ser missense_variant 0.22
ethA 4328243 c.-770C>A upstream_gene_variant 0.2
ethA 4328343 c.-870C>T upstream_gene_variant 0.17
ethA 4328358 c.-885C>G upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338660 c.-139G>A upstream_gene_variant 0.25
gid 4407765 c.438G>A synonymous_variant 0.17
gid 4407879 c.324G>T synonymous_variant 0.12