TB-Profiler result

Run: SRR1173597
Summary

Run ID: SRR1173597

Sample name:

Date: 03-04-2023 03:28:23

Number of reads: 1260863

Percentage reads mapped: 85.1

Strain: lineage1.2.2.2

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 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 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 6728 c.-574C>T upstream_gene_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 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 0.97
mshA 576038 p.Asp231Asn missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
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
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.11
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.11
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.13
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.14
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.13
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.31
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.3
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.3
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.3
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.31
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.31
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.11
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.11
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.1
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.11
rrs 1473070 n.1225G>C non_coding_transcript_exon_variant 0.1
rrs 1473071 n.1226C>A non_coding_transcript_exon_variant 0.1
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.22
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.22
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.22
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.22
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.19
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.18
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.2
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.2
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.98
PPE35 2169320 p.Leu431Phe missense_variant 0.21
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
thyX 3067724 c.222G>A synonymous_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.12
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
Rv3236c 3612368 p.Thr250Met missense_variant 1.0
rpoA 3877887 c.621G>A synonymous_variant 0.19
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
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 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
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 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
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