TB-Profiler result

Run: ERR11050239
Summary

Run ID: ERR11050239

Sample name:

Date: 02-04-2023 17:43:10

Number of reads: 733449

Percentage reads mapped: 99.25

Strain: lineage1.1.3.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.99
lineage1.1.3.2 Indo-Oceanic NA RD239 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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491315 p.Gly178Ala missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576365 p.Phe340Ile missense_variant 0.18
mshA 576483 p.Val379Gly missense_variant 1.0
mshA 576489 p.Val381Gly missense_variant 0.67
mshA 576606 p.Ala420Gly missense_variant 0.5
mshA 576609 p.Ala421Gly missense_variant 0.33
mshA 576702 p.Arg452Pro missense_variant 0.29
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
ccsA 620019 c.129A>C synonymous_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763150 p.Phe1115Cys missense_variant 0.17
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.27
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775735 p.Phe916Leu missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.47
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 1.0
fbiC 1303967 p.Leu346Arg missense_variant 0.22
Rv1258c 1406973 p.Ala123Gly missense_variant 1.0
embR 1416430 c.918G>C synonymous_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461104 c.60C>G synonymous_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.29
fabG1 1674065 p.Lys209Thr missense_variant 0.33
inhA 1674883 p.Ile228Val missense_variant 1.0
rpsA 1833388 c.-154C>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917986 p.Leu16Gln missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168065 p.Thr850Ala missense_variant 0.12
PPE35 2168466 c.2146delC frameshift_variant 0.11
PPE35 2170386 p.Leu76Arg missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288959 p.Tyr95His missense_variant 0.11
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.46
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746207 c.1392C>T synonymous_variant 1.0
pepQ 2859933 c.486C>G synonymous_variant 0.5
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064823 p.Val457Leu missense_variant 0.31
thyX 3067944 p.Val1Gly missense_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339047 c.-71G>C upstream_gene_variant 0.2
Rv3083 3448393 c.-111G>A upstream_gene_variant 0.11
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449357 p.Asn285Ser missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474047 p.Ser14Trp missense_variant 0.17
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640885 p.Arg115Cys missense_variant 0.17
fbiA 3641336 p.Val265Gly missense_variant 0.3
fbiB 3641536 c.2T>C start_lost 0.15
fbiB 3642173 c.639G>A synonymous_variant 1.0
fbiB 3642772 p.Asp413Gly missense_variant 0.18
alr 3840357 p.Leu355Arg missense_variant 0.17
alr 3840718 p.Ser235Ala missense_variant 0.14
rpoA 3878143 p.Gly122Asp missense_variant 0.22
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243013 p.Asp1051His missense_variant 0.15
embA 4243344 p.Gln38Lys missense_variant 0.14
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244837 c.1605G>A synonymous_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.18
embB 4247016 p.Ser168Trp missense_variant 0.67
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267203 p.Lys545Met missense_variant 0.15
aftB 4267314 c.1522dupA frameshift_variant 0.13
aftB 4267400 c.1437G>C synonymous_variant 0.31
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338200 p.Asp108His missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408003 p.Asp67Val missense_variant 0.2