TB-Profiler result

Run: SRR11349176
Summary

Run ID: SRR11349176

Sample name:

Date: 02-04-2023 20:54:12

Number of reads: 6478487

Percentage reads mapped: 90.95

Strain: lineage3

Drug-resistance: RR-TB

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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
lineage3 East-African-Indian CAS RD750 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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
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 8056 p.Arg252Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.31
mshA 576482 p.Val379Leu missense_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.32
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.32
rrs 1472972 n.1127T>A non_coding_transcript_exon_variant 0.3
rrs 1472974 n.1130_1133delTGGT non_coding_transcript_exon_variant 0.29
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.28
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.29
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.28
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.28
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.27
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.25
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.25
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.2
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.15
rrl 1475102 n.1445C>A non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.14
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.14
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.23
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.23
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.19
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.26
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.22
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.22
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.25
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.24
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.16
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.14
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.14
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.14
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.2
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.14
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.21
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0