TB-Profiler result

Run: ERR2229519
Summary

Run ID: ERR2229519

Sample name:

Date: 31-03-2023 17:16:47

Number of reads: 452668

Percentage reads mapped: 99.1

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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 5882 p.Gln215Lys missense_variant 0.17
gyrB 6266 p.Pro343Thr missense_variant 0.22
gyrB 6349 p.Gln370His missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7745 c.444G>A synonymous_variant 0.2
gyrA 8522 c.1221G>A synonymous_variant 0.17
gyrA 9306 p.Asp669Asn missense_variant 0.15
fgd1 491534 p.Pro251Leu missense_variant 0.18
rpoB 760346 p.Tyr180* stop_gained 0.29
rpoB 762486 p.Pro894Thr missense_variant 0.22
rpoB 762872 p.Met1022Ile missense_variant 0.2
rpoB 762879 p.Met1025Leu missense_variant 0.15
rpoB 762889 p.His1028Leu missense_variant 0.15
rpoC 762899 c.-471G>C upstream_gene_variant 0.17
rpoC 762920 c.-450C>T upstream_gene_variant 0.15
rpoC 762923 c.-447C>G upstream_gene_variant 0.14
rpoC 762929 c.-441G>C upstream_gene_variant 0.12
rpoC 762947 c.-423C>G upstream_gene_variant 0.14
rpoC 762962 c.-408C>T upstream_gene_variant 0.15
rpoC 762989 c.-381G>C upstream_gene_variant 0.15
rpoC 762995 c.-375G>C upstream_gene_variant 0.17
rpoC 763402 c.33C>T synonymous_variant 0.14
rpoC 763774 c.405G>A synonymous_variant 0.2
rpoC 764688 p.Gln440Arg missense_variant 0.2
rpoC 764768 p.Gln467Lys missense_variant 0.33
rpoC 764996 p.Val543Leu missense_variant 0.18
rpoC 765339 p.Gln657Pro missense_variant 0.22
rpoC 765989 c.2623delC frameshift_variant 0.33
rpoC 767267 c.3900delC frameshift_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776080 p.Ala801Ser missense_variant 0.33
mmpL5 776081 c.2400G>A synonymous_variant 0.33
mmpL5 776945 p.Glu512Asp missense_variant 0.17
mmpL5 777157 c.1324C>A synonymous_variant 0.22
mmpL5 777164 c.1317C>T synonymous_variant 0.25
mmpL5 777551 c.930G>T synonymous_variant 0.13
mmpL5 778089 p.Gly131Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801373 p.Asn189Tyr missense_variant 0.12
rplC 801379 p.Val191Leu missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304665 c.1735C>T synonymous_variant 0.18
fbiC 1304889 c.1959G>T synonymous_variant 0.4
fbiC 1305061 p.Gly711Trp missense_variant 0.25
Rv1258c 1406691 p.Arg217Leu missense_variant 0.15
Rv1258c 1406756 c.585T>C synonymous_variant 0.12
atpE 1461002 c.-43G>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472760 n.915G>T non_coding_transcript_exon_variant 0.15
rrs 1473014 n.1169G>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474602 n.945C>G non_coding_transcript_exon_variant 0.4
rrl 1475347 n.1690A>G non_coding_transcript_exon_variant 0.18
rrl 1475529 n.1872A>T non_coding_transcript_exon_variant 0.22
fabG1 1673231 c.-209G>T upstream_gene_variant 0.14
fabG1 1673436 c.-4C>A upstream_gene_variant 0.4
fabG1 1673717 p.Ala93Glu missense_variant 0.18
rpsA 1834845 c.1313_1315delCCG disruptive_inframe_deletion 0.33
rpsA 1834880 p.Asp447Asn missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155225 p.Met296Thr missense_variant 0.22
katG 2155344 c.768C>A synonymous_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169287 c.1326T>C synonymous_variant 0.14
PPE35 2169717 p.Asn299Ile missense_variant 0.15
PPE35 2169979 p.Val212Phe missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170147 p.Ser156Ala missense_variant 0.23
PPE35 2170157 p.Ala152Ser missense_variant 0.27
PPE35 2170247 p.Ile122Met missense_variant 0.12
PPE35 2170259 p.Ile118Val missense_variant 0.12
PPE35 2170266 p.Gly116Asp missense_variant 0.13
PPE35 2170270 p.Ser115Ala missense_variant 0.15
PPE35 2170280 c.333C>G synonymous_variant 0.14
Rv1979c 2222255 p.Ile304Val missense_variant 0.22
Rv1979c 2223167 c.-3G>T upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289622 c.-381C>A upstream_gene_variant 0.15
pncA 2289721 c.-480C>T upstream_gene_variant 0.25
pncA 2289749 c.-508G>C upstream_gene_variant 0.4
pncA 2290005 c.-764G>A upstream_gene_variant 0.18
eis 2714871 c.462G>A synonymous_variant 0.29
ahpC 2725959 c.-234C>T upstream_gene_variant 0.17
ahpC 2726442 p.Gly84Trp missense_variant 0.29
folC 2747097 p.Val168Phe missense_variant 0.25
folC 2747137 c.462G>T synonymous_variant 0.17
Rv2752c 3065081 p.His371Asp missense_variant 0.17
Rv2752c 3066030 p.Glu54Asp missense_variant 0.5
Rv2752c 3066094 p.Val33Ala missense_variant 0.25
thyX 3067579 p.Glu123Gln missense_variant 0.22
thyX 3067733 c.213G>A synonymous_variant 0.2
ald 3086997 p.Thr60Ala missense_variant 0.12
fbiD 3339102 c.-16C>A upstream_gene_variant 0.2
fbiD 3339129 c.12A>C synonymous_variant 0.17
fprA 3474061 p.Ala19Thr missense_variant 0.25
fprA 3474069 c.63C>T synonymous_variant 0.25
fprA 3474465 c.459C>T synonymous_variant 0.29
fprA 3475275 p.Trp423Cys missense_variant 0.33
fbiA 3640389 c.-154C>A upstream_gene_variant 0.18
fbiA 3641059 p.Trp173Gly missense_variant 0.33
fbiA 3641449 p.Val303Met missense_variant 0.13
fbiB 3641511 c.-24G>T upstream_gene_variant 0.25
alr 3840683 c.738G>A synonymous_variant 0.17
alr 3841362 p.Thr20Met missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.14
rpoA 3878057 p.Gln151Lys missense_variant 0.2
ddn 3986804 c.-40C>G upstream_gene_variant 0.29
clpC1 4040774 c.-71delC upstream_gene_variant 0.12
panD 4043994 c.288C>T synonymous_variant 0.4
embC 4240379 p.Gln173Lys missense_variant 0.33
embC 4242060 p.Ala733Glu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244169 p.Gln313Lys missense_variant 0.2
embA 4245266 c.2034C>T synonymous_variant 0.18
embA 4245733 p.Pro834Gln missense_variant 0.22
embB 4247470 c.957T>C synonymous_variant 0.18
embB 4247472 p.Phe320Tyr missense_variant 0.18
embB 4248490 c.1977G>T synonymous_variant 0.14
embB 4248829 c.2316T>C synonymous_variant 0.2
ethA 4326033 p.Ala481Ser missense_variant 0.15
ethA 4326053 p.Asp474Gly missense_variant 0.14
ethA 4326227 p.Thr416Asn missense_variant 0.2
ethA 4328343 c.-870C>A upstream_gene_variant 0.18
ethA 4328440 c.-967G>A upstream_gene_variant 0.22
whiB6 4338502 p.Ala7Val missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407589 p.Ala205Val missense_variant 0.25
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0