TB-Profiler result

Run: ERR233353
Summary

Run ID: ERR233353

Sample name:

Date: 13-08-2022 03:10:08

Number of reads: 8508764

Percentage reads mapped: 98.0

Strain: lineage1.2.2.1

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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.21
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.498A>C synonymous_variant 0.14
gyrA 8445 p.Arg382Gly missense_variant 0.25
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 491742 c.960T>C synonymous_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.23
rpoB 761285 c.1479G>C synonymous_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.15
rpoC 764751 p.Val461Gly missense_variant 0.31
rpoC 764905 p.Phe512Leu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406358 p.Ile328Thr missense_variant 0.15
Rv1258c 1406750 c.591C>A synonymous_variant 0.16
Rv1258c 1407240 p.Val34Gly missense_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417233 c.115C>T synonymous_variant 0.13
rrs 1471658 n.-188T>G upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.13
rrs 1473360 n.1515T>G non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.12
inhA 1674892 p.Asn231Asp missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168205 p.Pro803Gln missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290023 c.-782A>C upstream_gene_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518891 c.777C>A synonymous_variant 0.14
kasA 2519234 p.Glu374Lys missense_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.24
ahpC 2725954 c.-239C>T upstream_gene_variant 0.35
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726550 p.Gln120Lys missense_variant 0.17
ahpC 2726737 p.Asp182Ala missense_variant 0.18
folC 2746186 c.1413G>C synonymous_variant 0.19
folC 2747218 p.Ile127Met missense_variant 0.14
Rv2752c 3065265 c.927C>G synonymous_variant 0.19
thyX 3067995 c.-50A>C upstream_gene_variant 0.15
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
fprA 3475280 p.Val425Gly missense_variant 0.29
Rv3236c 3612804 p.Ala105Thr missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.24
rpoA 3877766 p.Ala248Pro missense_variant 0.22
rpoA 3878641 c.-135delG upstream_gene_variant 0.18
clpC1 4039363 p.Ala448Pro missense_variant 0.21
clpC1 4039932 p.Gly258Val missense_variant 0.28
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044307 c.-26A>G upstream_gene_variant 1.0
embC 4239870 p.Thr3Asn missense_variant 0.16
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.25
embC 4242476 p.Pro872Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.22
embA 4243532 c.300C>A synonymous_variant 1.0
embA 4243977 p.Ala249Pro missense_variant 0.21
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246275 p.Ala1015Thr missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269469 p.Pro122Gln missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.15
whiB6 4338588 c.-67C>T 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 4407873 c.330G>T synonymous_variant 1.0
gid 4408124 p.Ala27Pro missense_variant 1.0