TB-Profiler result

Run: ERR028356

Summary

Run ID: ERR028356

Sample name:

Date: 31-03-2023 08:23:33

Number of reads: 682648

Percentage reads mapped: 98.12

Strain: lineage4.1;lineage1.1.1.1

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 0.35
lineage1 Indo-Oceanic EAI RD239 0.08
lineage4.1 Euro-American T;X;H None 0.14
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.09
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.1
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.07
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.1
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 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.31
gyrA 9143 c.1842T>C synonymous_variant 0.24
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9437 c.2136G>A synonymous_variant 0.2
gyrA 9557 c.2256G>C synonymous_variant 0.21
fgd1 490972 p.Arg64Ser missense_variant 0.27
fgd1 491417 p.Arg212Gln missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 0.63
rpoC 762836 c.-534C>G upstream_gene_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 0.53
rpoC 763884 p.Ala172Val missense_variant 0.33
rpoC 763886 c.517C>A synonymous_variant 0.3
rpoC 765150 p.Gly594Glu missense_variant 0.11
rpoC 765171 p.Pro601Leu missense_variant 0.26
rpoC 766288 c.2919C>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.67
mmpL5 776182 p.Asp767Asn missense_variant 0.27
mmpL5 777581 p.Tyr300* stop_gained 0.42
mmpR5 778298 c.-692C>T upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154_-153insC upstream_gene_variant 0.19
rpsL 781421 c.-139C>A upstream_gene_variant 0.19
fbiC 1304610 c.1680C>T synonymous_variant 0.36
Rv1258c 1406750 c.591C>A synonymous_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.21
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.41
rrl 1475332 n.1675G>T non_coding_transcript_exon_variant 0.27
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.17
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.15
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.15
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.13
inhA 1673526 c.-676G>A upstream_gene_variant 0.2
fabG1 1673564 p.Val42Gly missense_variant 0.36
rpsA 1833909 p.Asp123Ala missense_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 0.35
rpsA 1834319 p.Val260Ile missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 0.76
PPE35 2167983 p.Gly877Asp missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.18
kasA 2518141 c.29dupG frameshift_variant 0.12
eis 2714225 p.Ala370Pro missense_variant 0.22
eis 2714366 p.Val323Leu missense_variant 0.29
eis 2715377 c.-45A>G upstream_gene_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 0.17
pepQ 2859904 p.Val172Gly missense_variant 0.22
ribD 2987172 p.Ser112Cys missense_variant 0.14
ribD 2987185 p.Gln116Leu missense_variant 0.13
Rv2752c 3064632 c.1560C>T synonymous_variant 0.25
thyA 3074654 c.-183T>G upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 0.21
Rv3083 3448714 p.Asp71His missense_variant 0.19
Rv3083 3448929 p.Tyr142* stop_gained 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 0.25
fprA 3475280 p.Val425Gly missense_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 0.56
alr 3840268 p.Thr385Pro missense_variant 0.31
rpoA 3878630 c.-124delC upstream_gene_variant 0.5
clpC1 4039932 p.Gly258Val missense_variant 0.27
clpC1 4040517 p.Val63Ala missense_variant 0.32
embC 4241042 p.Asn394Asp missense_variant 0.5
embC 4241429 p.Phe523Val missense_variant 0.5
embC 4242425 p.Arg855Gly missense_variant 0.29
embC 4242476 p.Pro872Ala missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.2
embA 4243460 c.228C>T synonymous_variant 0.33
embA 4243848 p.Val206Met missense_variant 0.21
embA 4244096 c.864C>T synonymous_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 0.2
aftB 4267272 p.Lys522Arg missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 0.5
ubiA 4269387 p.Glu149Asp missense_variant 0.38
ubiA 4269529 p.Ala102Gly missense_variant 0.38
aftB 4269606 c.-770T>C upstream_gene_variant 0.19
ethR 4326739 c.-810G>C upstream_gene_variant 0.2
ethA 4327672 c.-199G>A upstream_gene_variant 0.25
whiB6 4338242 p.Gln94Glu missense_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.33
gid 4407588 c.615A>G synonymous_variant 0.64
gid 4407790 p.Ala138Val missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 0.36