TB-Profiler result

Run: SRR1172797
Summary

Run ID: SRR1172797

Sample name:

Date: 03-04-2023 03:10:34

Number of reads: 1750050

Percentage reads mapped: 93.37

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 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
gid 4407967 p.Leu79Ser missense_variant 1.0 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
gyrB 5786 p.Thr183Ala missense_variant 1.0
gyrB 5981 p.Ser248Gly missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
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
Rv1258c 1406242 p.Ala367Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.11
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.1
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.1
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.1
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.11
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.11
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.11
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.18
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.17
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.12
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.12
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.11
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.11
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.11
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156400 c.-289G>A upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.23
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 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0