TB-Profiler result

Run: ERR1950080
Summary

Run ID: ERR1950080

Sample name:

Date: 31-03-2023 15:39:19

Number of reads: 502223

Percentage reads mapped: 99.31

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 5488 c.249C>A synonymous_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8382 p.Leu361Met missense_variant 0.11
mshA 576752 p.Pro469Ser missense_variant 0.22
rpoB 760235 c.429T>C synonymous_variant 0.11
rpoB 763285 p.Leu1160Pro missense_variant 0.14
rpoB 763325 c.3519A>C stop_lost&splice_region_variant 0.17
rpoC 763924 c.555G>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776011 p.Gln824* stop_gained 0.18
mmpL5 776788 p.Glu565* stop_gained 0.17
mmpR5 778355 c.-635G>T upstream_gene_variant 0.12
mmpL5 779022 c.-542G>C upstream_gene_variant 0.11
mmpR5 779055 p.Gln22His missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303613 p.Leu228Pro missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304513 p.Val528Asp missense_variant 0.11
fbiC 1305009 c.2079C>A synonymous_variant 0.15
Rv1258c 1406749 p.Lys198Glu missense_variant 0.11
Rv1258c 1407322 p.Gly7Arg missense_variant 0.1
atpE 1460964 c.-81C>G upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473963 n.306G>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474289 n.632C>T non_coding_transcript_exon_variant 0.14
rrl 1474300 n.643C>T non_coding_transcript_exon_variant 0.15
rrl 1475955 n.2298A>G non_coding_transcript_exon_variant 0.12
fabG1 1673368 c.-72A>T upstream_gene_variant 0.11
inhA 1674226 c.28_34delATTCTGG frameshift_variant 0.2
rpsA 1834414 c.873C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918370 p.Ile144Asn missense_variant 0.13
ndh 2103089 c.-47C>A upstream_gene_variant 0.14
katG 2155089 p.Trp341* stop_gained 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169022 p.Gly531Trp missense_variant 0.4
PPE35 2169063 p.Met517Lys missense_variant 0.33
PPE35 2169593 c.1020C>A synonymous_variant 0.18
Rv1979c 2222431 p.Met245Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289027 p.Cys72Phe missense_variant 0.13
kasA 2519243 p.Asp377Asn missense_variant 0.12
eis 2715288 c.45G>T synonymous_variant 0.22
ahpC 2726269 p.Val26Asp missense_variant 0.24
fprA 3474702 c.696C>T synonymous_variant 0.12
fbiB 3641361 c.-174C>T upstream_gene_variant 0.18
alr 3841207 p.His72Tyr missense_variant 0.11
clpC1 4038705 p.Asn667Ser missense_variant 0.12
clpC1 4039121 c.1584T>G synonymous_variant 0.2
embC 4241427 p.Leu522Gln missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243160 c.-73C>G upstream_gene_variant 0.12
embA 4243584 p.Phe118Leu missense_variant 0.18
embB 4248486 p.Ser658Ile missense_variant 0.11
embB 4248505 c.1995delG frameshift_variant 0.12
embB 4248531 p.Phe673Ser missense_variant 0.11
embB 4248563 p.Ala684Thr missense_variant 0.11
embB 4249169 p.Asn886Asp missense_variant 0.13
aftB 4268286 p.Leu184Pro missense_variant 0.11
aftB 4268477 c.360C>G synonymous_variant 0.5
ubiA 4269137 p.Tyr233Asp missense_variant 0.5
ubiA 4269652 p.Val61Ala missense_variant 0.14
ubiA 4269701 p.Arg45Ser missense_variant 0.2
ubiA 4269715 p.Leu40Trp missense_variant 0.2
ubiA 4269919 c.-86T>C upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407722 p.Ala161Thr missense_variant 0.25
gid 4407839 p.Ser122Pro missense_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0