TB-Profiler result

Run: SRR5535926
Summary

Run ID: SRR5535926

Sample name:

Date: 04-04-2023 10:45:24

Number of reads: 1091208

Percentage reads mapped: 98.64

Strain: lineage1.2.2.2

Drug-resistance: HR-TB

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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
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.99
lineage1.2.2.2 Indo-Oceanic NA 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
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674262 p.Ile21Val missense_variant 0.91 isoniazid
katG 2154641 p.Gly491Cys missense_variant 0.18 isoniazid
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 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8064 p.Gly255* stop_gained 0.13
gyrA 8452 p.Ala384Val missense_variant 0.91
gyrA 8564 c.1263G>T synonymous_variant 0.19
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 576355 c.1008G>T synonymous_variant 0.2
mshA 576631 p.Phe428Leu missense_variant 0.15
rpoB 759928 p.Pro41Gln missense_variant 0.15
rpoB 761208 p.Asp468Tyr missense_variant 0.12
rpoB 761342 p.Lys512Asn missense_variant 0.17
rpoB 761704 p.Gly633Val missense_variant 0.11
rpoB 762731 p.Gln975His missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763158 p.Leu1118Met missense_variant 0.17
rpoC 763552 c.183C>T synonymous_variant 0.91
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764174 p.Asp269Tyr missense_variant 0.17
rpoC 764701 c.1332C>A synonymous_variant 0.15
rpoC 767091 p.Arg1241His missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779625 c.-720G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801440 p.Ala211Val missense_variant 0.17
Rv1258c 1407072 p.Pro90His missense_variant 0.29
Rv1258c 1407091 p.Ala84Thr missense_variant 0.5
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473087 n.1242A>C non_coding_transcript_exon_variant 0.2
rrl 1473717 n.60G>T non_coding_transcript_exon_variant 0.22
rrl 1476486 n.2830delG non_coding_transcript_exon_variant 0.18
fabG1 1673545 p.Ala36Ser missense_variant 0.33
inhA 1674510 p.Met103Ile missense_variant 0.25
rpsA 1834486 p.Glu315Asp missense_variant 0.14
tlyA 1917952 p.Ala5Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918072 p.Ala45Ser missense_variant 0.2
ndh 2102240 p.Arg268His missense_variant 1.0
ndh 2102286 p.Asp253Tyr missense_variant 0.18
ndh 2102589 p.Leu152Met missense_variant 0.15
ndh 2103089 c.-47C>G upstream_gene_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154961 p.Leu384Pro missense_variant 0.22
katG 2155391 p.Pro241Thr missense_variant 0.17
katG 2155932 c.180G>A synonymous_variant 0.15
PPE35 2167742 c.2871C>A synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 0.92
PPE35 2167969 p.Pro882Thr missense_variant 0.2
PPE35 2168009 c.2604C>T synonymous_variant 0.17
PPE35 2168742 p.Gly624Asp missense_variant 0.89
PPE35 2170296 p.Gln106Pro missense_variant 0.3
PPE35 2170681 c.-69G>T upstream_gene_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288821 p.Gln141Lys missense_variant 0.13
pncA 2289036 p.Pro69Gln missense_variant 0.16
pncA 2290109 c.-868C>A upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715156 c.177C>A synonymous_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859609 c.810G>A synonymous_variant 0.22
thyA 3074462 p.Tyr4Asp missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 0.9
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474145 p.Gly47Trp missense_variant 0.22
fprA 3474337 p.Met111Val missense_variant 0.14
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475179 p.Glu391Asp missense_variant 0.19
fbiB 3642632 c.1098C>T synonymous_variant 0.12
alr 3840582 p.Ala280Asp missense_variant 0.13
alr 3840666 p.Arg252Leu missense_variant 0.15
clpC1 4038215 c.2490G>T synonymous_variant 0.12
clpC1 4040513 p.Glu64Asp missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 0.94
panD 4044037 p.Gly82Val missense_variant 0.15
embC 4240162 c.300C>T synonymous_variant 0.88
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
embA 4245478 p.Met749Arg missense_variant 0.15
embA 4245670 p.Ala813Gly missense_variant 1.0
embB 4245794 c.-720G>T upstream_gene_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246979 p.Gly156Cys missense_variant 1.0
embB 4247113 c.600G>T synonymous_variant 0.14
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249652 p.His1047Asn missense_variant 0.17
aftB 4267960 p.Val293Met missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326080 p.Ile465Asn missense_variant 0.12
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4327420 p.Ser18Arg missense_variant 0.11
ethA 4328461 c.-988C>T upstream_gene_variant 0.13
whiB6 4338203 p.Arg107Cys missense_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 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0