TB-Profiler result

Run: SRR11444077
Summary

Run ID: SRR11444077

Sample name:

Date: 02-04-2023 21:02:54

Number of reads: 4934918

Percentage reads mapped: 88.42

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 8897 c.1596T>C synonymous_variant 0.11
gyrA 8909 c.1608C>T synonymous_variant 0.11
gyrA 8915 c.1614A>G synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 0.99
rpoB 760196 c.390C>G synonymous_variant 0.11
rpoB 760235 c.429T>C synonymous_variant 0.12
rpoB 760244 c.438G>C synonymous_variant 0.12
rpoB 760298 c.492G>C synonymous_variant 0.12
rpoB 760310 c.504G>C synonymous_variant 0.14
rpoB 760316 c.510C>G synonymous_variant 0.12
rpoB 760325 c.519G>C synonymous_variant 0.12
rpoB 760376 p.Asp190Glu missense_variant 0.12
rpoB 760430 c.624T>C synonymous_variant 0.11
rpoB 760460 c.654G>C synonymous_variant 0.13
rpoB 760484 c.678A>G synonymous_variant 0.12
rpoB 761249 c.1443A>G synonymous_variant 0.13
rpoB 761261 c.1455G>T synonymous_variant 0.12
rpoB 761264 c.1458C>G synonymous_variant 0.14
rpoB 761327 c.1521A>G synonymous_variant 0.11
rpoC 763666 c.297G>A synonymous_variant 0.12
rpoC 763675 c.306C>G synonymous_variant 0.11
rpoC 763699 c.330G>T synonymous_variant 0.12
rpoC 764746 c.1377G>T synonymous_variant 0.12
rpoC 764911 c.1542A>G synonymous_variant 0.12
rpoC 764912 p.Met515Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.12
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.14
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.13
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.13
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.13
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.19
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.15
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.14
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.12
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.13
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.12
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.19
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.18
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.18
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.21
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.19
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.16
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.15
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.12
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.12
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12
rpsA 1833838 c.297G>C synonymous_variant 0.11
rpsA 1833841 c.300C>G synonymous_variant 0.12
rpsA 1833847 c.306C>G synonymous_variant 0.12
rpsA 1833856 c.315A>G synonymous_variant 0.11
rpsA 1833859 c.318C>G synonymous_variant 0.11
rpsA 1833874 c.333T>C synonymous_variant 0.15
rpsA 1833894 p.Ala118Glu missense_variant 0.12
rpsA 1833994 c.453G>C synonymous_variant 0.12
rpsA 1834000 c.459G>C synonymous_variant 0.12
rpsA 1834015 c.474G>C synonymous_variant 0.11
rpsA 1834021 c.480C>T synonymous_variant 0.14
rpsA 1834030 c.489C>G synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289037 p.Pro69Ser missense_variant 0.99
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
clpC1 4039682 c.1023C>G synonymous_variant 0.12
embC 4240783 c.921G>C synonymous_variant 0.13
embC 4240789 c.927T>C synonymous_variant 0.12
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 0.89