TB-Profiler result

Run: SRR10272570
Summary

Run ID: SRR10272570

Sample name:

Date: 02-04-2023 16:38:41

Number of reads: 719333

Percentage reads mapped: 86.99

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 0.97
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
gyrB 7106 p.Glu623Lys missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7986 p.Pro229Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491494 c.713dupA frameshift_variant 0.13
fgd1 491717 p.Ala312Val missense_variant 0.14
mshA 576412 c.1065C>T synonymous_variant 0.25
mshA 576751 p.Lys468Asn missense_variant 0.4
ccsA 619831 c.-60T>G upstream_gene_variant 0.29
ccsA 620007 c.117T>C synonymous_variant 0.15
ccsA 620728 p.His280Asn missense_variant 0.12
rpoB 762325 p.Lys840Arg missense_variant 0.13
rpoB 763222 p.Ile1139Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779193 c.-713G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781831 p.Pro91His missense_variant 0.13
fbiC 1303850 p.Pro307His missense_variant 0.13
fbiC 1304970 c.2040G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472157 n.312A>T non_coding_transcript_exon_variant 0.12
rrs 1472373 n.528G>T non_coding_transcript_exon_variant 0.18
rrl 1474498 n.841G>A non_coding_transcript_exon_variant 0.2
rrl 1474522 n.865C>A non_coding_transcript_exon_variant 0.17
rrl 1475193 n.1536C>G non_coding_transcript_exon_variant 0.11
inhA 1674498 c.297G>C synonymous_variant 0.14
inhA 1674849 p.Gln216His missense_variant 0.13
rpsA 1834012 c.471G>A synonymous_variant 0.12
rpsA 1834015 c.474G>C synonymous_variant 0.12
rpsA 1834018 c.477C>T synonymous_variant 0.12
rpsA 1834024 c.483G>C synonymous_variant 0.12
rpsA 1834034 p.Ile165Val missense_variant 0.12
rpsA 1834039 c.498C>T synonymous_variant 0.12
rpsA 1834040 p.Lys167Gln missense_variant 0.12
rpsA 1834069 c.528G>C synonymous_variant 0.12
rpsA 1834090 c.549G>T synonymous_variant 0.14
rpsA 1834099 c.558C>G synonymous_variant 0.17
rpsA 1834827 p.Thr429Asn missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155006 p.Gly369Val missense_variant 0.14
katG 2155414 p.Glu233Gly missense_variant 0.13
katG 2156527 c.-417delG upstream_gene_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.14
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169602 c.1011C>A synonymous_variant 0.13
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169890 c.723C>T synonymous_variant 0.18
PPE35 2169893 c.720C>A synonymous_variant 0.18
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.57
PPE35 2170147 p.Ser156Ala missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290036 c.-795C>T upstream_gene_variant 0.15
pncA 2290169 c.-928C>T upstream_gene_variant 0.15
ahpC 2726732 p.Lys180Asn missense_variant 0.18
folC 2746512 p.Ala363Pro missense_variant 0.11
folC 2746692 p.Val303Met missense_variant 0.15
pepQ 2859375 c.1044G>T synonymous_variant 0.14
ribD 2986825 c.-14C>T upstream_gene_variant 0.13
thyX 3067745 c.201C>A synonymous_variant 0.12
thyA 3073949 p.Pro175Ala missense_variant 0.17
thyA 3074514 c.-43T>C upstream_gene_variant 0.18
thyA 3074554 c.-83G>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449713 p.Ala404Ser missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474014 p.Pro3Leu missense_variant 0.33
fprA 3474058 p.Ala18Thr missense_variant 0.2
fprA 3474160 p.Gly52Trp missense_variant 0.12
fprA 3475295 p.Glu430Gly missense_variant 0.4
Rv3236c 3612155 p.Arg321Leu missense_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641951 c.417G>T synonymous_variant 0.2
fbiB 3642655 p.Thr374Lys missense_variant 0.15
alr 3841187 c.234C>A synonymous_variant 0.12
alr 3841565 c.-145G>T upstream_gene_variant 0.12
clpC1 4038444 p.Ala754Glu missense_variant 0.2
clpC1 4039184 c.1521G>T synonymous_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.12
clpC1 4040151 p.Gly185Val missense_variant 0.12
clpC1 4040244 p.Gly154Val missense_variant 0.14
clpC1 4040265 p.Gly147Val missense_variant 0.14
clpC1 4040898 c.-194C>A upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244284 p.Pro351Leu missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.21
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.21
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246567 c.54G>T synonymous_variant 0.19
embB 4247225 p.Arg238Cys missense_variant 0.15
embB 4247769 p.Ile419Thr missense_variant 0.2
embB 4247814 p.Ala434Val missense_variant 0.17
embB 4249323 p.Ala937Glu missense_variant 0.25
embB 4249731 p.Ala1073Val missense_variant 0.15
ethA 4326241 p.Asp411Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0