TB-Profiler result

Run: SRR4035736
Summary

Run ID: SRR4035736

Sample name:

Date: 04-04-2023 07:16:06

Number of reads: 1488228

Percentage reads mapped: 99.41

Strain: lineage4.1.2

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
gyrB 5749 c.510G>T synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490838 p.Glu19Val missense_variant 0.13
fgd1 490983 c.201G>A synonymous_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576444 p.Gly366Ala missense_variant 0.17
mshA 576477 p.Leu377Gln missense_variant 0.2
mshA 576724 c.1377G>A synonymous_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761340 p.Lys512Glu missense_variant 0.12
rpoB 761903 c.2097T>C synonymous_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764545 c.1176C>A synonymous_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776079 p.Ala801Gly missense_variant 0.11
mmpL5 776662 p.Leu607Phe missense_variant 0.14
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801150 c.342G>A synonymous_variant 0.15
Rv1258c 1407062 c.279G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472844 n.999C>T non_coding_transcript_exon_variant 0.12
rrl 1473935 n.278C>T non_coding_transcript_exon_variant 0.14
inhA 1674930 c.729C>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918248 c.309T>A synonymous_variant 0.12
ndh 2103195 c.-153C>T upstream_gene_variant 0.12
katG 2155435 p.Gly226Ala missense_variant 0.1
katG 2156108 p.Pro2Ala missense_variant 0.11
katG 2156368 c.-259_-258delTC upstream_gene_variant 0.16
PPE35 2170507 p.Thr36Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288994 p.Pro83His missense_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518582 c.468G>A synonymous_variant 0.13
kasA 2518600 c.486C>T synonymous_variant 0.17
eis 2714852 p.Ser161Arg missense_variant 0.12
ribD 2987124 p.Val96Ile missense_variant 0.13
Rv2752c 3066094 p.Val33Asp missense_variant 0.15
Rv2752c 3066105 c.87C>G synonymous_variant 0.12
thyX 3067927 c.19C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087905 c.1086G>C synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474592 p.Ile196Phe missense_variant 0.15
fprA 3474624 c.618G>T synonymous_variant 0.14
fprA 3474919 p.Lys305* stop_gained 0.2
fprA 3474965 p.Arg320Pro missense_variant 0.13
fprA 3475202 p.Pro399Gln missense_variant 0.13
fprA 3475243 p.Arg413Cys missense_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
alr 3841598 c.-178C>G upstream_gene_variant 0.11
panD 4043977 p.Gln102Arg missense_variant 0.12
panD 4043980 p.Tyr101Cys missense_variant 0.12
embC 4239815 c.-48C>T upstream_gene_variant 0.18
embC 4241552 p.Pro564* stop_gained 0.13
embA 4242469 c.-764C>T upstream_gene_variant 0.15
embC 4242491 p.Arg877Trp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246643 p.Thr44Ala missense_variant 0.12
embB 4249143 p.Val877Glu missense_variant 0.14
embB 4249152 p.Ala880Val missense_variant 0.14
embB 4249399 c.2886G>C synonymous_variant 0.11
embB 4249600 c.3087A>G synonymous_variant 0.13
embB 4249608 p.Thr1032Ile missense_variant 0.13
aftB 4267338 p.Leu500Pro missense_variant 0.17
aftB 4268850 c.-14T>A upstream_gene_variant 0.12
ethA 4326071 p.Ile468Thr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407533 p.Ala224Thr missense_variant 0.12
gid 4408273 c.-71C>G upstream_gene_variant 0.11