TB-Profiler result

Run: ERR4821194

Summary

Run ID: ERR4821194

Sample name:

Date: 01-04-2023 17:06:57

Number of reads: 1173830

Percentage reads mapped: 98.9

Strain: lineage4.1.2.1

Drug-resistance: Sensitive


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 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 5357 p.Arg40Cys missense_variant 0.11
gyrB 6614 p.Glu459* stop_gained 0.12
gyrB 6747 p.Gln503Arg missense_variant 0.2
gyrB 6839 p.Asp534Tyr missense_variant 0.11
gyrA 7351 p.Pro17Leu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7815 p.Asn172Asp missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490816 p.Ala12Ser missense_variant 0.11
fgd1 490824 p.Gln14His missense_variant 0.13
fgd1 490916 c.138_140dupCCA disruptive_inframe_insertion 0.15
fgd1 491292 c.510G>A synonymous_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575384 p.Ile13Val missense_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762287 c.2481C>G synonymous_variant 0.14
rpoB 762293 c.2487T>C synonymous_variant 0.14
rpoB 762317 c.2511A>G synonymous_variant 0.12
rpoB 762320 c.2514C>G synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765583 c.2214G>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775743 p.Gly913Asp missense_variant 0.12
mmpL5 777350 c.1131G>T synonymous_variant 0.11
mmpL5 777458 p.Ile341Met missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781416 c.-144C>A upstream_gene_variant 0.25
rplC 800920 p.Arg38Cys missense_variant 0.17
rplC 801182 p.Gly125Asp missense_variant 0.13
fbiC 1303350 p.Cys140* stop_gained 0.13
Rv1258c 1406384 c.957G>A synonymous_variant 0.12
embR 1416222 p.Phe376Leu missense_variant 0.18
embR 1416232 p.Cys372Gly missense_variant 0.15
embR 1416495 p.Gly285Ser missense_variant 0.12
embR 1416533 p.Gly272Val missense_variant 0.12
atpE 1460875 c.-170C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.29
rrl 1473404 n.-254C>G upstream_gene_variant 0.25
rrl 1476768 n.3111G>A non_coding_transcript_exon_variant 0.22
inhA 1673571 c.-631C>T upstream_gene_variant 0.2
inhA 1673631 c.-571C>T upstream_gene_variant 0.13
fabG1 1673786 p.Ala116Glu missense_variant 0.13
inhA 1673913 c.-289C>T upstream_gene_variant 0.13
fabG1 1673941 c.505delC frameshift_variant 0.17
rpsA 1833477 c.-65C>A upstream_gene_variant 0.18
rpsA 1834459 c.918G>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153926 p.Asp729Gly missense_variant 0.12
katG 2155800 c.312G>T synonymous_variant 0.12
PPE35 2168282 p.Asp777Glu missense_variant 0.13
PPE35 2169479 c.1134C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518202 p.Glu30* stop_gained 0.33
folC 2746439 p.Val387Ala missense_variant 0.14
folC 2746952 p.Lys216Arg missense_variant 0.12
ribD 2986702 c.-137G>T upstream_gene_variant 0.15
Rv2752c 3067171 c.-980C>G upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087058 p.Ala80Gly missense_variant 0.11
ald 3087302 c.487delG frameshift_variant 0.18
ald 3087551 c.732C>A synonymous_variant 0.17
Rv3083 3449604 c.1101G>T synonymous_variant 0.15
Rv3083 3449815 p.Gln438Lys missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474319 p.Gly105Ser missense_variant 0.17
fprA 3474645 c.639C>T synonymous_variant 0.11
fprA 3475282 p.Ile426Val missense_variant 0.15
Rv3236c 3612997 c.119delG frameshift_variant 0.2
fbiA 3640844 p.Trp101* stop_gained 0.17
alr 3840293 c.1128T>C synonymous_variant 0.13
alr 3841166 c.255T>C synonymous_variant 0.12
rpoA 3877485 p.Tyr341* stop_gained 0.14
rpoA 3877591 p.Leu306Pro missense_variant 0.12
rpoA 3878169 c.339G>T synonymous_variant 0.12
rpoA 3878234 p.Pro92Thr missense_variant 0.14
clpC1 4038887 p.Glu606Asp missense_variant 0.17
clpC1 4039957 p.Leu250Val missense_variant 0.11
clpC1 4040894 c.-190G>T upstream_gene_variant 0.14
panD 4044049 p.Leu78Ser missense_variant 0.1
embC 4241557 c.1695C>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245121 p.Tyr630Phe missense_variant 0.14
embA 4245410 c.2178C>T synonymous_variant 0.12
embA 4245445 p.Asp738Gly missense_variant 0.11
embB 4247316 p.Leu268Pro missense_variant 1.0
embB 4247685 p.Leu391Ser missense_variant 0.11
embB 4248279 p.Pro589His missense_variant 0.14
embB 4248321 p.Gly603Glu missense_variant 0.12
embB 4249793 p.Ile1094Val missense_variant 0.18
aftB 4268577 p.Ala87Val missense_variant 0.17
aftB 4268855 c.-19G>T upstream_gene_variant 0.3
ubiA 4269166 p.Thr223Met missense_variant 0.11
ethA 4328283 c.-810G>T upstream_gene_variant 0.11
ethA 4328332 c.-860delC upstream_gene_variant 0.17
ethA 4328351 c.-878C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407616 p.Leu196Trp missense_variant 0.12
gid 4408424 c.-222C>T upstream_gene_variant 0.12