TB-Profiler result

Run: ERR028317
Summary

Run ID: ERR028317

Sample name:

Date: 31-03-2023 08:21:49

Number of reads: 800403

Percentage reads mapped: 99.15

Strain: lineage6;lineage5.1;lineage4.2.2;lineage1.1.3.1;lineage1.1.1

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 0.42
lineage1 Indo-Oceanic EAI RD239 0.33
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.07
lineage6 West-Africa 2 AFRI_1 RD702 0.05
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.25
lineage5.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.06
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.06
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.09
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.13
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.06
lineage1.1.3.1 Indo-Oceanic NA RD239 0.06
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 5081 c.-159G>C upstream_gene_variant 0.21
gyrB 5698 c.459G>A synonymous_variant 0.18
gyrB 6112 p.Met291Ile missense_variant 0.33
gyrB 6446 p.Ala403Ser missense_variant 0.3
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7538 p.Glu79Asp missense_variant 0.12
gyrA 7539 p.Thr80Ala missense_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.38
gyrA 9143 c.1842T>C synonymous_variant 0.52
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9629 c.2328C>T synonymous_variant 0.12
fgd1 490751 c.-32T>G upstream_gene_variant 0.12
fgd1 491668 p.Lys296Glu missense_variant 0.1
fgd1 491742 c.960T>C synonymous_variant 0.5
mshA 575679 p.Asn111Ser missense_variant 0.2
rpoB 759831 p.Thr9Pro missense_variant 0.48
rpoB 761723 p.Glu639Asp missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.61
rpoC 763884 p.Ala172Val missense_variant 0.43
rpoC 763886 c.517C>A synonymous_variant 0.43
rpoC 765171 p.Pro601Leu missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775753 c.2727delC frameshift_variant 0.3
mmpL5 776100 p.Thr794Ile missense_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.33
embR 1417019 p.Cys110Tyr missense_variant 0.44
atpE 1461083 c.39T>G synonymous_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.2
inhA 1673338 c.-864G>A upstream_gene_variant 0.14
rpsA 1834299 p.Gln253Arg missense_variant 0.13
rpsA 1834319 p.Val260Ile missense_variant 0.12
rpsA 1834631 p.Gln364Lys missense_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.15
ndh 2103112 c.-70G>T upstream_gene_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 0.79
PPE35 2167926 p.Leu896Ser missense_variant 0.46
PPE35 2167983 p.Gly877Asp missense_variant 0.32
PPE35 2169379 p.Phe412Val missense_variant 0.33
PPE35 2169866 c.747G>C synonymous_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 0.64
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289622 c.-381C>T upstream_gene_variant 0.19
pncA 2290062 c.-821G>A upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 0.7
kasA 2518675 p.Met187Ile missense_variant 0.15
ahpC 2725954 c.-239C>T upstream_gene_variant 0.29
ahpC 2726051 c.-142G>A upstream_gene_variant 0.24
pepQ 2860436 c.-18C>T upstream_gene_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 0.28
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.3
thyX 3067976 c.-31T>G upstream_gene_variant 0.29
thyA 3073806 c.666C>G synonymous_variant 0.5
thyA 3074654 c.-183T>G upstream_gene_variant 0.18
ald 3086705 c.-115T>G upstream_gene_variant 0.17
ald 3086742 c.-78A>C upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 0.5
ald 3087084 c.266delA frameshift_variant 0.27
fbiD 3339153 p.Leu12Phe missense_variant 0.19
fbiD 3339335 p.Ala73Gly missense_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 0.43
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474256 p.Val84Phe missense_variant 0.12
fprA 3474597 c.591C>A synonymous_variant 0.43
fprA 3475159 p.Asn385Asp missense_variant 0.58
Rv3236c 3612422 p.Val232Gly missense_variant 0.43
Rv3236c 3612665 p.Val151Ala missense_variant 0.17
alr 3840932 c.489C>T synonymous_variant 0.21
alr 3841498 c.-78A>G upstream_gene_variant 0.17
rpoA 3877696 p.Thr271Ile missense_variant 0.24
rpoA 3878238 p.Asp90Glu missense_variant 0.2
ddn 3986987 c.144G>T synonymous_variant 0.4
ddn 3987180 p.Asp113Asn missense_variant 0.14
clpC1 4038857 c.1848C>A synonymous_variant 0.25
clpC1 4039932 p.Gly258Val missense_variant 0.33
clpC1 4040517 p.Val63Ala missense_variant 0.47
clpC1 4040824 c.-120C>T upstream_gene_variant 0.38
embC 4239843 c.-20A>C upstream_gene_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.33
embC 4241011 c.1149C>T synonymous_variant 0.13
embC 4241042 p.Asn394Asp missense_variant 0.22
embC 4241429 p.Phe523Val missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.33
embA 4244096 c.864C>T synonymous_variant 0.31
embA 4245147 p.Pro639Ser missense_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 0.43
embB 4246164 c.-350T>C upstream_gene_variant 0.19
embB 4247646 p.Glu378Ala missense_variant 0.5
embB 4248725 p.Ser738Ala missense_variant 0.27
ubiA 4269387 p.Glu149Asp missense_variant 0.67
aftB 4269606 c.-770T>C upstream_gene_variant 0.75
ethR 4326928 c.-621G>A upstream_gene_variant 0.12
ethA 4327103 p.Gly124Asp missense_variant 0.17
ethA 4328329 c.-856C>G upstream_gene_variant 0.1
whiB6 4338242 p.Gln94Glu missense_variant 0.33
whiB6 4338546 c.-25G>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.4
gid 4407588 c.615A>G synonymous_variant 0.62
gid 4407780 c.423G>A synonymous_variant 0.12
gid 4407873 c.330G>T synonymous_variant 0.46