TB-Profiler result

Run: SRR4035499
Summary

Run ID: SRR4035499

Sample name:

Date: 04-04-2023 07:07:56

Number of reads: 896601

Percentage reads mapped: 99.67

Strain: lineage4.4.1.1.1

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 0.99
lineage4.4.1.1.1 Euro-American S;Orphans None 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
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 576249 p.Pro301Leu missense_variant 0.17
rpoB 760062 p.Glu86Gln missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775914 p.Ala856Val missense_variant 0.11
mmpL5 778240 p.Val81Leu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.15
fbiC 1303760 p.Ile277Thr missense_variant 0.11
fbiC 1303995 c.1065C>T synonymous_variant 0.18
fbiC 1304420 p.Ala497Val missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.18
rpsA 1833970 c.429G>A synonymous_variant 0.1
rpsA 1834980 p.Ser480Ile missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918626 c.687G>A synonymous_variant 0.13
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168075 c.2538G>A synonymous_variant 0.11
PPE35 2169320 p.Leu431Phe missense_variant 0.2
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289878 c.-637C>G upstream_gene_variant 0.14
pncA 2290132 c.-891C>T upstream_gene_variant 0.15
ribD 2987303 c.465G>T synonymous_variant 0.1
ribD 2987307 p.Ala157Pro missense_variant 0.27
thyX 3067206 p.Ala247Val missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339056 c.-62A>G upstream_gene_variant 0.11
fbiD 3339412 p.Ala99Thr missense_variant 0.17
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
clpC1 4038928 c.1774_1776delTCG conservative_inframe_deletion 0.11
clpC1 4039343 c.1362G>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243697 c.468delC frameshift_variant 0.14
embA 4243830 c.603_604dupGC frameshift_variant 0.11
embA 4244277 p.Pro349Ser missense_variant 0.14
embA 4246261 c.3031delC frameshift_variant 0.14
embB 4246768 c.255C>T synonymous_variant 0.14
embB 4249019 p.Gly836Trp missense_variant 0.12
embB 4249368 p.Asp952Gly missense_variant 0.22
embB 4249520 p.Ala1003Thr missense_variant 0.11
ethA 4326749 p.Asn242Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0