TB-Profiler result

Run: SRR2099939
Summary

Run ID: SRR2099939

Sample name:

Date: 03-04-2023 22:38:17

Number of reads: 2415355

Percentage reads mapped: 99.58

Strain: lineage3.1.2.2

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
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
lineage3.1.2.2 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
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
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760475 c.669A>G synonymous_variant 0.1
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763670 p.Val101Phe missense_variant 0.12
rpoC 763853 p.Val162Ile missense_variant 0.11
rpoC 764058 p.Ala230Val missense_variant 0.13
rpoC 766699 p.Gln1110His missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776532 p.Ala650Val missense_variant 0.12
mmpL5 777321 p.Val387Ala missense_variant 0.14
mmpL5 777977 c.504G>A synonymous_variant 0.14
mmpL5 778944 c.-464C>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406637 p.Val235Ala missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476669 n.3012C>T non_coding_transcript_exon_variant 0.29
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
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2170433 c.180G>T synonymous_variant 0.11
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
pncA 2289500 c.-259A>G upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859424 p.Gly332Val missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087476 c.657C>T synonymous_variant 1.0
fbiD 3339115 c.-3T>C upstream_gene_variant 0.14
fbiD 3339176 p.Ala20Val missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475259 p.Val418Ala missense_variant 0.14
fbiA 3641144 p.Ala201Val missense_variant 0.12
fbiB 3642747 p.Ala405Ser missense_variant 0.12
alr 3841206 p.His72Leu missense_variant 0.11
clpC1 4038226 p.Pro827Thr missense_variant 0.11
embC 4240478 p.Gly206Arg missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242128 c.2266C>T synonymous_variant 0.11
embC 4242627 p.Ala922Val missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246268 c.-246G>A upstream_gene_variant 0.11
embB 4248212 p.Ala567Ser missense_variant 0.12
embB 4248372 p.Arg620Pro missense_variant 0.11
embB 4248858 c.2346delA frameshift_variant 0.11
embB 4248874 c.2361C>A synonymous_variant 0.11
ethA 4326176 p.Glu433Ala missense_variant 1.0
ethA 4327591 c.-118G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0