TB-Profiler result

Run: SRR10272564
Summary

Run ID: SRR10272564

Sample name:

Date: 02-04-2023 16:39:49

Number of reads: 887220

Percentage reads mapped: 86.54

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
mshA 575457 p.Asn37Ser missense_variant 0.13
mshA 576466 c.1119G>A synonymous_variant 0.17
mshA 576579 p.Gly411Val missense_variant 0.12
rpoB 760703 c.897C>A synonymous_variant 0.12
rpoB 761152 p.Leu449Gln missense_variant 0.13
rpoB 761518 p.Asp571Val missense_variant 0.11
rpoC 766790 p.Val1141Phe missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778244 c.-746G>A upstream_gene_variant 0.2
mmpR5 779315 p.Arg109Gln missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303518 p.Met196Ile missense_variant 0.12
embR 1416891 p.Leu153Met missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.11
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.15
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.15
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.15
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
fabG1 1674118 p.Glu227Lys missense_variant 0.14
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.13
rpsA 1834456 c.915T>C synonymous_variant 0.13
rpsA 1834459 c.918G>C synonymous_variant 0.13
rpsA 1834468 c.927A>G synonymous_variant 0.13
rpsA 1834474 c.933C>G synonymous_variant 0.13
rpsA 1834483 p.Glu314Asp missense_variant 0.12
rpsA 1834489 c.948T>C synonymous_variant 0.12
rpsA 1834528 c.987T>C synonymous_variant 0.2
rpsA 1834534 c.993C>G synonymous_variant 0.2
rpsA 1834538 p.Val333Ile missense_variant 0.2
rpsA 1834546 p.Asp335Glu missense_variant 0.2
rpsA 1834552 c.1011G>C synonymous_variant 0.2
rpsA 1834555 c.1014T>G synonymous_variant 0.29
rpsA 1834556 p.Ala339Gln missense_variant 0.29
rpsA 1834603 p.Glu354Asp missense_variant 0.4
rpsA 1834609 c.1068T>C synonymous_variant 1.0
rpsA 1834612 c.1071G>C synonymous_variant 1.0
rpsA 1834619 c.1078T>C synonymous_variant 1.0
rpsA 1834633 c.1092A>G synonymous_variant 1.0
rpsA 1834639 c.1098T>C synonymous_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 0.94
PPE35 2169939 p.Gly225Ala missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.21
PPE35 2170385 c.228G>T synonymous_variant 0.19
PPE35 2170392 p.Gly74Ala missense_variant 0.27
PPE35 2170400 c.213G>C synonymous_variant 0.29
PPE35 2170412 c.201G>A synonymous_variant 0.14
PPE35 2170415 c.198A>G synonymous_variant 0.14
PPE35 2170434 p.Arg60Ala missense_variant 0.11
PPE35 2170436 c.177T>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289896 c.-655C>T upstream_gene_variant 0.12
kasA 2518879 c.765A>G synonymous_variant 0.29
kasA 2518882 c.768C>A synonymous_variant 0.29
kasA 2519153 p.Ile347Val missense_variant 0.17
ribD 2987559 p.Ala241Thr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448632 c.130delA frameshift_variant 0.12
Rv3083 3449016 c.513A>G synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475044 c.1038C>T synonymous_variant 0.18
Rv3236c 3612155 p.Arg321Leu missense_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
clpC1 4038284 p.Trp807* stop_gained 0.15
clpC1 4038381 p.Arg775His missense_variant 0.12
clpC1 4039691 c.1014G>C synonymous_variant 0.12
clpC1 4039714 p.Tyr331His missense_variant 0.19
embC 4241296 c.1434C>T synonymous_variant 0.12
embC 4241611 c.1749G>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0