TB-Profiler result

Run: ERR3994093
Summary

Run ID: ERR3994093

Sample name:

Date: 01-04-2023 03:42:04

Number of reads: 310852

Percentage reads mapped: 99.71

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2155849 p.Gln88Arg missense_variant 0.12 isoniazid
pncA 2288779 p.Val155Leu missense_variant 0.18 pyrazinamide
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 5490 p.Ile84Thr missense_variant 0.22
gyrB 5860 p.Asn207Lys missense_variant 0.12
gyrB 5888 p.Glu217* stop_gained 0.13
gyrB 6230 p.Tyr331Asn missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7475 c.174A>G synonymous_variant 0.2
gyrA 7695 p.Ala132Thr missense_variant 0.15
gyrA 7876 p.His192Leu missense_variant 0.22
mshA 575482 c.135C>A synonymous_variant 0.4
ccsA 620712 c.822G>T synonymous_variant 0.18
rpoB 760048 p.Glu81Val missense_variant 0.12
rpoB 760318 p.Ser171Thr missense_variant 0.1
rpoB 760636 p.Pro277Arg missense_variant 0.13
rpoB 761159 c.1353G>A synonymous_variant 0.13
rpoB 761195 c.1389G>C synonymous_variant 0.2
rpoB 761297 c.1491C>T synonymous_variant 0.18
rpoB 761465 c.1659G>T synonymous_variant 0.18
rpoB 761775 p.Asp657Tyr missense_variant 0.22
rpoC 763923 p.Glu185Gly missense_variant 0.17
rpoC 763941 p.Ala191Asp missense_variant 0.15
rpoC 764851 p.His494Gln missense_variant 0.25
rpoC 764991 c.1624dupG frameshift_variant 0.2
rpoC 766432 c.3063T>C synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777126 p.Ser452Ile missense_variant 0.2
mmpL5 778280 p.Asp67Glu missense_variant 0.22
mmpS5 778764 p.Pro48Ala missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781502 c.-58G>A upstream_gene_variant 0.25
rpsL 781506 c.-54C>G upstream_gene_variant 0.25
rpsL 781763 c.204C>T synonymous_variant 0.15
fbiC 1303336 p.Ala136Ser missense_variant 0.12
fbiC 1303909 p.Pro327Ala missense_variant 0.17
fbiC 1304501 p.Ala524Glu missense_variant 0.29
Rv1258c 1406633 c.708C>G synonymous_variant 0.4
Rv1258c 1407316 p.Ala9Thr missense_variant 0.12
Rv1258c 1407381 c.-41G>T upstream_gene_variant 0.22
embR 1417209 p.Asn47Asp missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471971 n.127_129delTCT non_coding_transcript_exon_variant 0.12
rrl 1473506 n.-152G>A upstream_gene_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474736 n.1079C>A non_coding_transcript_exon_variant 0.12
rrl 1475530 n.1873C>G non_coding_transcript_exon_variant 0.17
rrl 1475729 n.2072C>G non_coding_transcript_exon_variant 0.14
rrl 1475821 n.2164T>C non_coding_transcript_exon_variant 0.17
fabG1 1673917 c.480_482delGAT disruptive_inframe_deletion 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918435 p.Ala166Thr missense_variant 0.18
ndh 2102688 p.Ala119Pro missense_variant 0.25
katG 2156384 c.-273G>A upstream_gene_variant 1.0
PPE35 2168917 p.Pro566Ala missense_variant 0.2
PPE35 2169445 c.1167delC frameshift_variant 0.15
PPE35 2169796 p.Gly273Cys missense_variant 0.14
PPE35 2170576 p.Ala13Ser missense_variant 0.25
Rv1979c 2221733 p.Pro478Ala missense_variant 0.15
Rv1979c 2222802 c.363C>G synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288825 c.417G>T synonymous_variant 0.22
folC 2746552 c.1046delT frameshift_variant 0.33
folC 2746929 p.Pro224Thr missense_variant 0.29
Rv2752c 3065684 p.Asp170Tyr missense_variant 0.14
ald 3086971 p.Lys51Arg missense_variant 0.18
ald 3087865 p.Ala349Val missense_variant 0.12
ald 3087870 p.Leu351Met missense_variant 0.12
fbiD 3339000 c.-117_-116delCA upstream_gene_variant 0.29
fprA 3475314 c.1308G>T synonymous_variant 0.15
Rv3236c 3612572 c.543G>C synonymous_variant 0.18
fbiA 3640948 c.408delG frameshift_variant 0.12
fbiA 3641247 c.706delG frameshift_variant 0.15
fbiB 3641929 c.400_401delGC frameshift_variant 0.22
fbiB 3642573 p.Val347Leu missense_variant 0.17
alr 3840764 c.657G>C synonymous_variant 1.0
clpC1 4038162 p.Arg848Pro missense_variant 0.12
clpC1 4038339 p.Ile789Asn missense_variant 0.17
clpC1 4038370 p.Arg779Cys missense_variant 0.2
clpC1 4038852 c.1849_1852delAAGC frameshift_variant 0.17
clpC1 4038917 c.1788C>A synonymous_variant 0.12
clpC1 4040862 c.-158C>A upstream_gene_variant 0.14
embC 4242172 c.2310C>G synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243492 p.Gly87Val missense_variant 0.17
embA 4244502 p.Gln424Glu missense_variant 0.12
embA 4244692 p.Tyr487Cys missense_variant 0.11
embA 4244721 p.Gln497Glu missense_variant 0.12
embA 4244727 p.Phe499Leu missense_variant 0.14
embA 4245002 c.1770C>T synonymous_variant 0.5
embA 4245176 c.1944G>T synonymous_variant 0.2
embB 4245893 c.-621C>T upstream_gene_variant 0.12
embB 4247422 c.910_912delCTG conservative_inframe_deletion 0.18
ethA 4326699 p.Arg259Gly missense_variant 0.12
ethA 4327383 p.Ser31Gly missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407631 p.Cys191Phe missense_variant 0.2