TB-Profiler result

Run: SRR6896312

Summary

Run ID: SRR6896312

Sample name:

Date: 04-04-2023 18:02:05

Number of reads: 532461

Percentage reads mapped: 99.64

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.99
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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 6095 c.857delA frameshift_variant 0.12
gyrB 6716 p.Ile493Val missense_variant 0.11
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8153 c.852C>T synonymous_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619973 c.94_96delCTG conservative_inframe_deletion 0.12
ccsA 620631 c.741T>A synonymous_variant 0.13
rpoB 760614 p.Asp270His missense_variant 0.12
rpoB 760834 p.His343Leu missense_variant 0.15
rpoB 763089 p.Lys1095Glu missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766040 p.Cys891Arg missense_variant 0.11
rpoC 766112 p.Tyr915His missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777537 p.Leu315Pro missense_variant 1.0
mmpR5 779048 p.Val20Ala missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303244 p.Cys105Tyr missense_variant 0.11
fbiC 1304746 c.1817delA frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471962 n.118dupC non_coding_transcript_exon_variant 0.11
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472354 n.509C>T non_coding_transcript_exon_variant 0.11
rrl 1473532 n.-126T>C upstream_gene_variant 0.17
rrl 1474415 n.758C>T non_coding_transcript_exon_variant 0.1
rrl 1475621 n.1964T>C non_coding_transcript_exon_variant 0.2
rrl 1476079 n.2422G>A non_coding_transcript_exon_variant 0.14
tlyA 1917854 c.-86A>G upstream_gene_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154099 c.2013G>A synonymous_variant 0.12
katG 2154492 p.Phe540Leu missense_variant 0.11
PPE35 2168147 c.2466A>G synonymous_variant 0.11
PPE35 2169087 p.Pro509Gln missense_variant 0.25
PPE35 2169754 p.Phe287Leu missense_variant 0.17
PPE35 2170774 c.-162T>C upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747389 c.210G>A synonymous_variant 0.11
Rv2752c 3067141 c.-950A>T upstream_gene_variant 0.14
thyX 3067442 c.504C>T synonymous_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073898 p.Ala192Thr missense_variant 0.12
thyA 3073925 c.547T>C synonymous_variant 0.11
thyA 3073985 p.Leu163Phe missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338968 c.-150A>G upstream_gene_variant 0.15
Rv3083 3449215 c.715delG frameshift_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640874 p.Thr111Ile missense_variant 0.1
fbiB 3642786 p.Trp418Gly missense_variant 0.22
rpoA 3877654 p.Asp285Val missense_variant 0.11
rpoA 3877665 c.843C>G synonymous_variant 0.1
rpoA 3878321 p.Phe63Leu missense_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038728 c.1977C>T synonymous_variant 0.14
clpC1 4039269 p.Val479Ala missense_variant 0.13
clpC1 4039879 p.Ile276Phe missense_variant 0.12
clpC1 4039930 p.Ser259Gly missense_variant 0.12
clpC1 4040397 p.Ile103Asn missense_variant 0.15
panD 4044089 p.Gly65Ser missense_variant 0.1
embC 4241667 p.Ala602Val missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244452 p.Pro407Gln missense_variant 0.11
embA 4245397 p.Asn722Ser missense_variant 0.12
embA 4246417 p.Arg1062Gln missense_variant 0.11
embB 4248636 p.Pro708Leu missense_variant 0.13
aftB 4267336 p.Asp501Asn missense_variant 0.12
aftB 4268093 c.744C>T synonymous_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0