TB-Profiler result

Run: ERR9891968

Summary

Run ID: ERR9891968

Sample name:

Date: 02-04-2023 13:25:23

Number of reads: 463392

Percentage reads mapped: 98.87

Strain: lineage4.6.2

Drug-resistance: Other


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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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 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
pncA 2288853 p.Val130Gly missense_variant 0.15 pyrazinamide
ethA 4327054 c.419delA frameshift_variant 0.17 ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7762 p.Pro154Arg missense_variant 1.0
gyrA 8551 p.Ala417Val missense_variant 0.12
gyrA 9226 p.Ser642Tyr missense_variant 0.15
gyrA 9245 c.1944C>A synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9464 c.2163C>A synonymous_variant 0.15
fgd1 491157 p.Phe125Leu missense_variant 0.25
fgd1 491193 c.411G>T synonymous_variant 0.22
fgd1 491429 p.Ala216Asp missense_variant 0.67
fgd1 491614 p.Glu278* stop_gained 0.2
fgd1 491631 c.849C>T synonymous_variant 0.2
rpoB 760443 p.Arg213Gly missense_variant 0.11
rpoB 761149 p.Arg448Leu missense_variant 0.2
rpoB 761184 p.Glu460* stop_gained 0.2
rpoB 762183 p.Gly793Trp missense_variant 0.2
rpoC 764452 c.1083T>G synonymous_variant 0.12
rpoC 764821 p.Trp484Cys missense_variant 0.15
rpoC 765000 c.1633delC frameshift_variant 0.18
rpoC 765674 p.Glu769* stop_gained 0.25
rpoC 765964 p.Leu865Phe missense_variant 0.4
rpoC 766820 p.Asp1151Tyr missense_variant 0.36
rpoC 767252 p.Pro1295Thr missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775937 c.2544G>T synonymous_variant 0.22
mmpL5 776600 c.1881G>T synonymous_variant 0.12
mmpR5 778067 c.-923G>C upstream_gene_variant 0.12
mmpR5 778088 c.-902C>A upstream_gene_variant 0.13
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
mmpL5 779196 c.-716G>T upstream_gene_variant 0.2
mmpL5 779244 c.-764G>T upstream_gene_variant 0.22
mmpL5 779400 c.-920C>A upstream_gene_variant 0.22
mmpS5 779506 c.-601C>A upstream_gene_variant 0.18
mmpS5 779582 c.-677C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800639 c.-170C>A upstream_gene_variant 0.15
rplC 800664 c.-145G>T upstream_gene_variant 0.12
rplC 800671 c.-138G>T upstream_gene_variant 0.17
rplC 800821 p.Gly5Cys missense_variant 0.14
rplC 800859 p.Phe17Leu missense_variant 0.15
fbiC 1303278 c.348C>A synonymous_variant 0.17
fbiC 1303304 p.Pro125His missense_variant 0.12
fbiC 1303355 p.Glu142Gly missense_variant 0.12
fbiC 1303719 c.789C>T synonymous_variant 0.17
fbiC 1304094 p.Met388Ile missense_variant 0.5
fbiC 1304631 p.Phe567Leu missense_variant 0.17
fbiC 1304679 p.Glu583Asp missense_variant 0.18
fbiC 1304885 p.Trp652Leu missense_variant 0.19
fbiC 1304924 p.Pro665Gln missense_variant 0.13
fbiC 1304946 c.2016G>T synonymous_variant 0.2
fbiC 1305094 p.His722Asn missense_variant 0.33
embR 1416417 p.Gly311Trp missense_variant 0.15
embR 1417151 p.Ser66Leu missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475165 n.1508G>T non_coding_transcript_exon_variant 0.25
fabG1 1673266 c.-174C>A upstream_gene_variant 0.22
inhA 1674376 p.Pro59Thr missense_variant 0.4
inhA 1674690 c.489C>A synonymous_variant 0.22
rpsA 1833515 c.-27C>A upstream_gene_variant 0.13
tlyA 1917888 c.-52C>A upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918209 c.270C>A synonymous_variant 0.67
ndh 2102874 p.Gln57Lys missense_variant 0.33
ndh 2103068 c.-26G>T upstream_gene_variant 0.15
katG 2154448 p.Ala555Val missense_variant 0.14
katG 2155471 p.Arg214Leu missense_variant 0.22
katG 2156046 c.66C>A synonymous_variant 0.25
katG 2156334 c.-223G>T upstream_gene_variant 0.18
katG 2156470 c.-360delT upstream_gene_variant 0.18
katG 2156510 c.-399C>A upstream_gene_variant 0.2
PPE35 2167970 p.Ile881Met missense_variant 0.13
PPE35 2168161 p.Glu818Lys missense_variant 0.17
PPE35 2168213 c.2400G>T synonymous_variant 0.33
PPE35 2170259 c.354A>T synonymous_variant 0.33
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289338 c.-97A>G upstream_gene_variant 0.4
pncA 2289501 c.-260G>T upstream_gene_variant 0.29
kasA 2519008 c.894C>A synonymous_variant 0.18
eis 2714772 c.561G>T synonymous_variant 0.18
eis 2714807 p.Glu176* stop_gained 0.25
eis 2715381 c.-49C>A upstream_gene_variant 0.18
ahpC 2725945 c.-248G>T upstream_gene_variant 0.22
ahpC 2725956 c.-237G>T upstream_gene_variant 0.22
ribD 2986669 c.-170G>T upstream_gene_variant 0.22
ribD 2986707 c.-132G>T upstream_gene_variant 0.13
ribD 2986772 c.-67C>T upstream_gene_variant 0.15
ribD 2987526 p.Gly230* stop_gained 0.33
Rv2752c 3065774 p.Glu140* stop_gained 0.25
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyX 3067984 c.-39C>A upstream_gene_variant 0.5
thyA 3074003 p.Gly157Cys missense_variant 0.12
ald 3087478 p.Ser220* stop_gained 0.14
fbiD 3339075 c.-43C>A upstream_gene_variant 0.33
fbiD 3339619 p.Ala168Ser missense_variant 0.33
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3449648 p.Pro382His missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612074 p.Ile348Ser missense_variant 1.0
Rv3236c 3612307 p.Phe270Leu missense_variant 0.29
Rv3236c 3612578 p.Glu180Gly missense_variant 0.4
Rv3236c 3613025 p.Ser31* stop_gained 0.15
Rv3236c 3613197 c.-81G>T upstream_gene_variant 0.17
fbiB 3640560 c.-975G>T upstream_gene_variant 0.15
fbiB 3640734 c.-801C>A upstream_gene_variant 0.4
fbiB 3641529 c.-6G>T upstream_gene_variant 0.29
fbiB 3641563 p.Ser10* stop_gained 0.22
alr 3841366 p.Gly19Cys missense_variant 0.18
ddn 3987138 p.Gln99Lys missense_variant 0.15
clpC1 4038889 p.Glu606* stop_gained 0.29
clpC1 4039783 p.Leu308Met missense_variant 0.13
clpC1 4040201 c.504C>A synonymous_variant 0.4
clpC1 4040428 p.Arg93Cys missense_variant 1.0
embC 4239706 c.-157A>G upstream_gene_variant 0.29
embC 4239892 c.30C>T synonymous_variant 0.22
embC 4240219 c.357C>A synonymous_variant 0.5
embC 4241909 p.Ala683Pro missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242787 c.-446G>T upstream_gene_variant 0.4
embA 4243336 p.Pro35Gln missense_variant 0.4
embA 4244081 c.849C>T synonymous_variant 0.67
embA 4244439 p.Gly403* stop_gained 0.4
embA 4244524 p.Pro431Gln missense_variant 0.67
embA 4244875 p.Pro548Gln missense_variant 1.0
embB 4248139 c.1626C>G synonymous_variant 0.2
embB 4248171 p.Ala553Glu missense_variant 0.12
embB 4248175 c.1662G>C synonymous_variant 0.12
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4267531 p.Ala436Ser missense_variant 0.33
aftB 4269315 c.-479C>A upstream_gene_variant 0.2
ubiA 4269589 p.Arg82Leu missense_variant 0.5
ubiA 4269981 c.-148G>A upstream_gene_variant 0.67
ethA 4326514 p.Phe320Leu missense_variant 0.17
ethA 4326603 p.Gln291Lys missense_variant 0.17
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4327547 c.-74C>A upstream_gene_variant 0.13
ethA 4327689 c.-216G>T upstream_gene_variant 0.29
ethA 4327776 c.-303C>A upstream_gene_variant 0.22
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
ethA 4328157 c.-684C>A upstream_gene_variant 0.33
ethA 4328233 c.-760G>A upstream_gene_variant 0.4
ethA 4328408 c.-935C>A upstream_gene_variant 0.2
ethA 4328437 c.-964G>T upstream_gene_variant 0.2
whiB6 4338359 p.Ala55Ser missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408284 c.-82G>T upstream_gene_variant 0.15