TB-Profiler result

Run: ERR2660479
Summary

Run ID: ERR2660479

Sample name:

Date: 31-03-2023 22:51:17

Number of reads: 1149113

Percentage reads mapped: 95.65

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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 6112 p.Met291Ile missense_variant 0.98
gyrB 6124 c.885C>T synonymous_variant 0.98
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.95
gyrA 9047 c.1746C>T synonymous_variant 0.97
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763781 p.Ser138Ala missense_variant 0.12
rpoC 763884 p.Ala172Val missense_variant 0.92
rpoC 763886 c.517C>A synonymous_variant 0.93
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765556 c.2187G>C synonymous_variant 0.12
rpoC 765580 c.2211G>C synonymous_variant 0.13
rpoC 765583 c.2214G>C synonymous_variant 0.13
rpoC 765625 c.2256C>G synonymous_variant 0.12
rpoC 765628 c.2259G>C synonymous_variant 0.12
rpoC 765658 c.2289C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406438 c.903A>C synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.19
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.19
rrl 1473966 n.309T>C non_coding_transcript_exon_variant 0.23
rrl 1473971 n.314G>T non_coding_transcript_exon_variant 0.23
rrl 1473981 n.324_325insT non_coding_transcript_exon_variant 0.2
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.18
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.18
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.2
rrl 1474036 n.379G>A non_coding_transcript_exon_variant 0.2
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.21
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.23
rrl 1474093 n.436G>A non_coding_transcript_exon_variant 0.19
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.12
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.12
rrl 1474110 n.453A>G non_coding_transcript_exon_variant 0.13
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.12
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.12
rrl 1474282 n.625G>A non_coding_transcript_exon_variant 0.12
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.17
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.12
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.2
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.25
rrl 1474961 n.1304T>G non_coding_transcript_exon_variant 0.25
rrl 1474963 n.1306G>A non_coding_transcript_exon_variant 0.22
rrl 1474964 n.1307T>C non_coding_transcript_exon_variant 0.22
rrl 1474969 n.1312G>A non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102290 c.753C>T synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 0.95
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
Rv2752c 3065484 c.708G>A synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_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 0.95
embC 4241162 c.1300T>C synonymous_variant 0.12
embC 4241188 c.1326C>T synonymous_variant 0.17
embC 4241227 c.1365G>A synonymous_variant 0.13
embC 4241228 c.1366_1368delCTAinsTTG synonymous_variant 0.13
embC 4241248 c.1386G>C synonymous_variant 0.16
embC 4241251 c.1389T>C synonymous_variant 0.16
embC 4241256 p.Arg465Thr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
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 4407717 c.485dupT frameshift_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0