TB-Profiler result

Run: SRR4037588

Summary

Run ID: SRR4037588

Sample name:

Date: 04-04-2023 07:31:49

Number of reads: 1480601

Percentage reads mapped: 99.6

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 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 5520 p.Pro94Leu missense_variant 1.0
gyrB 7160 p.Ala641Thr missense_variant 0.2
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 9304 p.Gly668Asp missense_variant 1.0
mshA 575222 c.-126C>A upstream_gene_variant 0.13
ccsA 620643 c.755_756dupAG frameshift_variant 0.14
rpoB 761608 c.1807dupG frameshift_variant 0.14
rpoB 761960 p.Met718Ile missense_variant 0.12
rpoC 762836 c.-534C>G upstream_gene_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767040 p.Ala1224Glu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777889 p.Gln198* stop_gained 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781876 c.318delT frameshift_variant 0.12
fbiC 1303458 c.528G>A synonymous_variant 0.12
Rv1258c 1407528 c.-188C>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475745 n.2088A>C non_coding_transcript_exon_variant 0.12
inhA 1674953 p.Pro251Gln missense_variant 0.18
rpsA 1833956 c.416delT frameshift_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102504 p.Pro180His missense_variant 0.12
PPE35 2169003 p.Leu537Ser missense_variant 0.13
PPE35 2169320 p.Leu431Phe missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290070 c.-829G>A upstream_gene_variant 0.11
eis 2714865 c.468C>T synonymous_variant 0.13
eis 2715007 p.Ala109Val missense_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.36
folC 2746605 p.Ala332Thr missense_variant 0.2
folC 2746864 c.735G>T synonymous_variant 0.13
ribD 2987415 p.Glu193Lys missense_variant 0.13
Rv2752c 3065468 p.Val242Met missense_variant 0.11
Rv2752c 3065762 p.Phe144Ile missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339270 c.153G>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641303 p.Gly254Asp missense_variant 0.11
fbiB 3641955 p.Gly141Arg missense_variant 0.14
alr 3841057 p.Pro122Ser missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.12
embC 4240708 c.846G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243403 p.Gln57His missense_variant 0.14
embA 4245618 p.Asp796Tyr missense_variant 0.12
embB 4245641 c.-873C>T upstream_gene_variant 0.12
embB 4249708 c.3195C>A synonymous_variant 0.13
aftB 4267279 p.Arg520Trp missense_variant 0.13
aftB 4267911 p.Pro309Gln missense_variant 0.2
aftB 4267938 c.898delC frameshift_variant 0.14
ethR 4327948 p.Val134Leu missense_variant 0.13
whiB6 4338448 c.73delG frameshift_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407842 c.359_360dupAG frameshift_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 1.0