TB-Profiler result

Run: SRR21677883
Summary

Run ID: SRR21677883

Sample name:

Date: 04-04-2023 02:49:41

Number of reads: 833680

Percentage reads mapped: 84.99

Strain: lineage4.1.1.2

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.2 Euro-American (X-type) X1 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.14 streptomycin
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
ccsA 619925 p.Arg12His missense_variant 0.13
rpoB 762943 p.Ile1046Asn missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775972 p.Ala837Ser missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302814 c.-117C>T upstream_gene_variant 1.0
fbiC 1304422 p.Ala498Ser missense_variant 0.17
fbiC 1304437 c.1508delA frameshift_variant 0.18
fbiC 1304442 c.1512T>C synonymous_variant 0.17
fbiC 1304443 p.Ala505Thr missense_variant 0.17
fbiC 1304446 c.1516_1517insT frameshift_variant 0.17
embR 1417008 c.339delG frameshift_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.14
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.1
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.1
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.1
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.13
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.12
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.12
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.13
rrs 1473291 n.1446G>A non_coding_transcript_exon_variant 0.13
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.13
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.13
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.15
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.15
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.15
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.17
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.12
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.13
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15
inhA 1674504 c.306dupG frameshift_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067534 p.Ala138Thr missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087792 p.Ala325Ser missense_variant 0.11
Rv3083 3449670 c.1167C>T synonymous_variant 0.11
Rv3083 3449787 c.1284C>T synonymous_variant 1.0
Rv3083 3449873 c.1371delG frameshift_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475010 p.Asp335Val missense_variant 0.12
rpoA 3878535 c.-28G>T upstream_gene_variant 0.15
rpoA 3878619 c.-113delC upstream_gene_variant 0.33
embC 4241572 c.1710C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243513 p.Pro94Gln missense_variant 0.12
embA 4243833 p.Ala201Thr missense_variant 1.0
embA 4244247 p.Val339Ile missense_variant 0.15
embA 4245555 p.Glu775* stop_gained 0.11
embB 4246544 p.Thr11Pro missense_variant 0.11
embB 4246930 p.Gln139His missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267792 p.Pro349Ala missense_variant 0.11
aftB 4267943 p.Tyr298* stop_gained 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0