TB-Profiler result

Run: SRR12199421
Summary

Run ID: SRR12199421

Sample name:

Date: 03-04-2023 06:38:34

Number of reads: 327834

Percentage reads mapped: 32.54

Strain: lineage1.1.3.1

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 0.98
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3.1 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
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 5122 c.-118_-117insC upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7496 c.195C>T synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8828 p.Asp509Glu missense_variant 0.25
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
rpoB 759767 c.-40G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763131 p.Pro1109Thr missense_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764541 p.Val391Asp missense_variant 0.2
rpoC 764731 c.1362G>A synonymous_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 0.67
mmpR5 778445 c.-545G>T upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781479 c.-81G>C upstream_gene_variant 0.14
fbiC 1302914 c.-17A>T upstream_gene_variant 0.33
fbiC 1303016 p.Val29Gly missense_variant 0.33
fbiC 1303660 p.Val244Phe missense_variant 0.33
Rv1258c 1406721 p.Gly207Glu missense_variant 1.0
Rv1258c 1407436 c.-96T>A upstream_gene_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471661 n.-185C>T upstream_gene_variant 0.17
rrs 1471670 n.-176G>A upstream_gene_variant 0.18
rrl 1473505 n.-153G>T upstream_gene_variant 0.12
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.13
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.13
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.13
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.13
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.13
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.13
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.14
rrl 1475745 n.2088A>T non_coding_transcript_exon_variant 0.12
fabG1 1673272 c.-168C>T upstream_gene_variant 0.22
rpsA 1834624 c.1083G>T synonymous_variant 0.5
ndh 2102653 p.His130Glu missense_variant 0.15
ndh 2102955 p.Ala30Thr missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156355 c.-244C>T upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168150 c.2463T>C synonymous_variant 0.11
PPE35 2169091 p.Val508Leu missense_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169308 c.1305C>T synonymous_variant 0.15
PPE35 2169890 c.723C>T synonymous_variant 0.12
PPE35 2169893 c.720C>A synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.38
PPE35 2170363 p.Glu84Gln missense_variant 0.4
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223356 c.-192C>T upstream_gene_variant 0.13
pncA 2288897 c.345A>G synonymous_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 0.8
eis 2714846 p.Val163Ile missense_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3066142 p.Arg17Gln missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086822 c.3G>C start_lost 0.15
ald 3087627 p.Asp270Asn missense_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449592 c.1089C>T synonymous_variant 0.18
Rv3083 3449956 p.Phe485Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474513 c.507T>C synonymous_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568660 p.Pro7Leu missense_variant 0.12
Rv3236c 3613006 p.Leu37Phe missense_variant 0.18
Rv3236c 3613080 p.Val13Ile missense_variant 0.12
fbiA 3640372 c.-171A>G upstream_gene_variant 0.56
fbiA 3641037 p.Lys165Asn missense_variant 0.18
alr 3840221 c.1200G>A synonymous_variant 0.18
alr 3840986 c.435G>A synonymous_variant 0.18
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.4
alr 3841612 c.-193_-192insC upstream_gene_variant 0.29
clpC1 4039730 c.975C>G synonymous_variant 0.18
clpC1 4039909 p.Glu266* stop_gained 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239978 p.Leu39Pro missense_variant 0.18
embC 4240648 c.786C>T synonymous_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242282 p.Ser807Ile missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244167 p.Ala312Val missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247512 c.999T>C synonymous_variant 0.17
embB 4247516 p.Asn335Asp missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267244 c.1593T>C synonymous_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C 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 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0