TB-Profiler result

Run: SRR3675460
Summary

Run ID: SRR3675460

Sample name:

Date: 04-04-2023 05:28:37

Number of reads: 512635

Percentage reads mapped: 74.62

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 763685 c.317delA frameshift_variant 0.12
rpoC 763699 c.333delC frameshift_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776754 p.Asp576Gly missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303123 p.Val65Leu missense_variant 0.13
Rv1258c 1406595 p.Lys249Arg missense_variant 0.12
Rv1258c 1406880 p.Phe154Ser missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.5
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.5
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.4
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.4
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.4
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.5
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.5
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.4
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.4
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.5
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.75
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.6
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.6
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.6
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.6
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.6
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.6
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.6
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 0.5
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.4
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.4
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.75
rpsA 1834984 c.1443T>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.23
katG 2156096 p.Pro6Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338970 c.-148C>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4241746 p.Phe628Leu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4327011 p.Glu155* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0