TB-Profiler result

Run: SRR6896229
Summary

Run ID: SRR6896229

Sample name:

Date: 04-04-2023 17:59:33

Number of reads: 442639

Percentage reads mapped: 96.66

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 None 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 2289224 p.Ile6Met missense_variant 0.12 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
gyrA 6751 c.-551G>T upstream_gene_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9300 p.Ala667Thr missense_variant 0.12
fgd1 490901 c.123delT frameshift_variant 0.13
fgd1 491531 p.Ala250Val missense_variant 0.11
mshA 575761 c.414C>T synonymous_variant 1.0
mshA 576004 c.657T>C synonymous_variant 0.14
rpoB 759814 p.Asp3Gly missense_variant 1.0
rpoC 764780 c.1411_1412delAGinsTC synonymous_variant 0.17
rpoC 764804 p.Gln479Phe missense_variant 0.14
rpoC 764809 c.1440C>T synonymous_variant 0.14
rpoC 764812 c.1443C>G synonymous_variant 0.14
rpoC 764815 c.1446A>G synonymous_variant 0.13
rpoC 764818 c.1449G>C synonymous_variant 0.13
rpoC 764824 c.1455T>C synonymous_variant 0.12
rpoC 764833 c.1464A>G synonymous_variant 0.13
rpoC 764843 p.Ala492Thr missense_variant 0.12
rpoC 764857 c.1488G>C synonymous_variant 0.11
rpoC 764858 c.1489T>C synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779349 c.-869C>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781502 c.-58G>T upstream_gene_variant 1.0
fbiC 1304534 p.Leu535Ser missense_variant 0.12
embR 1416772 c.576C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.1
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.1
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.11
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.11
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.11
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.11
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.11
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.1
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.1
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.11
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.11
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.12
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.11
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.11
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.11
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.11
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
rpsA 1833372 c.-170C>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169041 c.1572G>A synonymous_variant 0.25
PPE35 2169044 c.1569G>C synonymous_variant 0.44
PPE35 2169047 p.Ile522Val missense_variant 0.29
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.29
PPE35 2169059 c.1554G>A synonymous_variant 0.71
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Ile missense_variant 0.71
PPE35 2169068 c.1545G>T synonymous_variant 0.71
PPE35 2169071 c.1542A>G synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289166 p.Ala26Ser missense_variant 0.13
ribD 2987111 p.Glu91Asp missense_variant 0.11
Rv2752c 3064832 p.Ala454Thr missense_variant 0.12
rpoA 3877512 c.996C>A synonymous_variant 0.1
embB 4249591 p.Asp1026Glu missense_variant 0.12
aftB 4267480 p.Pro453Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0