TB-Profiler result

Run: ERR3588246
Summary

Run ID: ERR3588246

Sample name:

Date: 01-04-2023 02:37:33

Number of reads: 741523

Percentage reads mapped: 98.38

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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
ethA 4327148 c.325dupT frameshift_variant 0.25 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 9105 p.Phe602Ser missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9405 p.Gly702Cys missense_variant 0.11
fgd1 491303 p.Ile174Thr missense_variant 0.15
fgd1 491363 p.Cys194Phe missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
ccsA 619755 c.-136T>C upstream_gene_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761410 p.Val535Ala missense_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766933 c.3564A>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776825 c.1656A>G synonymous_variant 0.11
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777543 p.Ser313* stop_gained 0.13
mmpL5 777709 p.Leu258Ile missense_variant 0.12
mmpL5 777764 c.717G>A synonymous_variant 0.13
mmpR5 779450 p.Leu154Pro missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781596 p.Arg13Trp missense_variant 0.12
fbiC 1303612 p.Leu228Ile missense_variant 1.0
fbiC 1304925 c.1995G>A synonymous_variant 0.12
embR 1416181 c.1167G>T stop_lost&splice_region_variant 0.2
embR 1416943 p.Ser135Arg missense_variant 0.1
embR 1417317 p.Leu11Val missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471997 n.152T>C non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.13
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.15
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.14
rrl 1474023 n.366T>C non_coding_transcript_exon_variant 0.4
rrl 1474641 n.984G>A non_coding_transcript_exon_variant 0.29
rrl 1475119 n.1462C>T non_coding_transcript_exon_variant 0.11
rrl 1475960 n.2303C>A non_coding_transcript_exon_variant 0.15
rrl 1476187 n.2530T>C non_coding_transcript_exon_variant 0.18
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.14
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.17
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.12
rrl 1476432 n.2777_2778delCC non_coding_transcript_exon_variant 0.11
inhA 1674447 c.246C>T synonymous_variant 0.17
tlyA 1917921 c.-19G>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102843 p.Glu67Gly missense_variant 0.12
katG 2155679 p.Arg145Cys missense_variant 0.12
PPE35 2168099 p.Gln838His missense_variant 0.11
PPE35 2168371 p.Ala748Thr missense_variant 1.0
PPE35 2169126 p.Val496Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289956 c.-715C>A upstream_gene_variant 0.29
pncA 2290169 c.-928C>A upstream_gene_variant 0.15
pncA 2290206 c.-965C>T upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726563 p.Val124Ala missense_variant 0.1
Rv2752c 3065477 p.Ala239Thr missense_variant 0.11
Rv2752c 3065554 p.Pro213Leu missense_variant 0.12
thyX 3068111 c.-166C>G upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339404 c.288delC frameshift_variant 0.14
fbiD 3339443 p.Asn109Ser missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474313 p.Ala103Ser missense_variant 0.15
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612032 p.Met362Thr missense_variant 0.12
Rv3236c 3612166 c.951A>G synonymous_variant 0.12
Rv3236c 3612409 c.708G>A synonymous_variant 0.12
rpoA 3878217 c.290delT frameshift_variant 0.12
rpoA 3878556 c.-49T>C upstream_gene_variant 0.33
embC 4241874 p.Leu671Arg missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244873 c.1641C>A synonymous_variant 0.14
embA 4244971 p.Leu580Pro missense_variant 0.14
aftB 4267216 p.Gly541* stop_gained 0.15
aftB 4267350 p.Met496Thr missense_variant 0.13
aftB 4267515 p.Ala441Glu missense_variant 0.11
ethA 4326899 p.Pro192Gln missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338636 c.-115C>T upstream_gene_variant 1.0