TB-Profiler result

Run: ERR2229632
Summary

Run ID: ERR2229632

Sample name:

Date: 31-03-2023 17:22:41

Number of reads: 705990

Percentage reads mapped: 99.28

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 6033 p.Asn265Thr missense_variant 0.22
gyrB 6569 p.Asp444Tyr missense_variant 0.12
gyrB 7188 p.Ile650Asn missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9683 c.2382G>T synonymous_variant 0.12
fgd1 491139 p.Glu119Asp missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576112 c.765C>G synonymous_variant 0.2
mshA 576488 p.Val381His missense_variant 0.4
mshA 576592 c.1245G>A synonymous_variant 0.15
mshA 576605 p.Ala420Ser missense_variant 0.18
rpoB 760722 p.Gly306Ser missense_variant 0.13
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 761292 p.Val496Met missense_variant 0.14
rpoB 761344 p.Val513Ala missense_variant 0.12
rpoB 762297 p.Leu831Met missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777595 p.Glu296* stop_gained 0.17
mmpL5 778057 p.Ser142Gly missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800972 p.Gly55Val missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304961 c.2031C>A synonymous_variant 0.12
embR 1416764 p.Glu195Gly missense_variant 0.12
embR 1416778 c.570G>C synonymous_variant 0.12
atpE 1461121 p.Ile26Asn missense_variant 0.4
atpE 1461285 p.Lys81* stop_gained 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472649 n.807delA non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474168 n.511A>G non_coding_transcript_exon_variant 0.33
rrl 1474389 n.732G>A non_coding_transcript_exon_variant 0.17
rrl 1475778 n.2121G>T non_coding_transcript_exon_variant 0.17
rrl 1475946 n.2289A>C non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.5
rrl 1476543 n.2886G>T non_coding_transcript_exon_variant 0.17
rpsA 1834542 p.Pro334Leu missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154980 c.1132C>T synonymous_variant 0.14
katG 2156123 c.-13delT upstream_gene_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.25
PPE35 2167868 c.2745A>C synonymous_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 0.14
PPE35 2167931 c.2682C>T synonymous_variant 0.13
PPE35 2168333 c.2280C>T synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168886 p.Leu576Pro missense_variant 0.12
PPE35 2169002 c.1611G>A synonymous_variant 0.22
PPE35 2169596 p.Phe339Val missense_variant 0.29
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2222764 p.Phe134Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288728 c.514C>T synonymous_variant 0.15
kasA 2518451 p.Gly113Ser missense_variant 0.14
eis 2714150 p.Pro395Thr missense_variant 0.15
ahpC 2726524 p.Leu111Pro missense_variant 0.12
folC 2746983 p.Gly206Ser missense_variant 0.15
folC 2747603 c.-5C>G upstream_gene_variant 0.15
Rv2752c 3067028 c.-837A>G upstream_gene_variant 0.1
thyX 3068122 c.-177C>A upstream_gene_variant 0.14
thyA 3073839 c.633T>C synonymous_variant 0.17
ald 3086636 c.-184A>T upstream_gene_variant 0.17
ald 3087066 p.Gly83Cys missense_variant 0.13
ald 3087636 p.Gly273Cys missense_variant 0.12
fbiD 3339491 p.Leu125Pro missense_variant 0.15
fprA 3474359 p.Asp118Val missense_variant 0.12
fprA 3474527 p.Ala174Glu missense_variant 0.22
Rv3236c 3612035 p.Val361Ala missense_variant 0.13
clpC1 4039248 p.Glu486Val missense_variant 0.12
clpC1 4040378 p.Leu109Phe missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243103 p.Thr1081Pro missense_variant 0.1
embA 4243303 p.Gly24Val missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4246563 p.Leu17Trp missense_variant 0.23
embB 4249527 p.Gly1005Val missense_variant 0.15
embB 4249536 p.Glu1008Gly missense_variant 0.15
aftB 4267127 c.1710G>A synonymous_variant 0.12
aftB 4267226 c.1611G>A synonymous_variant 0.12
aftB 4268792 c.45G>T synonymous_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.18
ethR 4326964 c.-585G>A upstream_gene_variant 0.25
ethR 4326970 c.-579G>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407544 p.Ser220Asn missense_variant 0.15
gid 4407846 c.357C>A synonymous_variant 0.14
gid 4408206 c.-4C>T upstream_gene_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0