TB-Profiler result

Run: SRR4036001
Summary

Run ID: SRR4036001

Sample name:

Date: 04-04-2023 07:25:58

Number of reads: 824074

Percentage reads mapped: 99.68

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 1.0
lineage4.4.1.1.1 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 5212 c.-28C>A upstream_gene_variant 0.15
gyrB 6748 p.Gln503His missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764370 p.Arg334Gln missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776354 c.2127C>G synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304419 p.Ala497Thr missense_variant 0.13
Rv1258c 1406982 p.Gly120Asp missense_variant 0.4
Rv1258c 1407149 c.192C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472546 n.701G>T non_coding_transcript_exon_variant 0.15
rrs 1472731 n.886C>T non_coding_transcript_exon_variant 0.15
rrl 1474319 n.662C>T non_coding_transcript_exon_variant 0.13
rrl 1476316 n.2659G>A non_coding_transcript_exon_variant 0.2
rpsA 1834169 c.630delC frameshift_variant 0.13
rpsA 1834978 c.1437C>A synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2156090 p.Ile8Phe missense_variant 0.11
katG 2156350 c.-239C>A upstream_gene_variant 0.12
PPE35 2167753 p.Ala954Thr missense_variant 0.13
PPE35 2169320 p.Leu431Phe missense_variant 0.33
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2222959 p.Ala69Val missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065183 p.Ser337Pro missense_variant 0.14
thyA 3073806 c.666C>G synonymous_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086961 p.Ala48Thr missense_variant 0.18
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449644 p.Ala381Thr missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612153 p.Gly322Trp missense_variant 0.18
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.25
embC 4242827 p.Leu989Val missense_variant 0.17
embB 4249072 c.2559G>A synonymous_variant 0.11
aftB 4269302 c.-466C>T upstream_gene_variant 0.15
ubiA 4269782 p.Val18Ile missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0