TB-Profiler result

Run: SRR12199408
Summary

Run ID: SRR12199408

Sample name:

Date: 03-04-2023 06:38:07

Number of reads: 947570

Percentage reads mapped: 78.68

Strain: lineage1

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 0.94
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 0.98
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 0.92
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 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490639 c.-144C>T upstream_gene_variant 0.77
fgd1 491742 c.960T>C synonymous_variant 1.0
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472870 n.1025T>C non_coding_transcript_exon_variant 1.0
rrl 1474910 n.1253C>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
inhA 1674390 c.189C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168140 p.Ala825Thr missense_variant 0.18
PPE35 2168742 p.Gly624Asp missense_variant 0.83
PPE35 2169041 c.1572G>A synonymous_variant 0.4
PPE35 2169044 c.1569G>C synonymous_variant 0.27
PPE35 2169053 c.1560T>C synonymous_variant 0.67
PPE35 2169059 c.1554G>A synonymous_variant 0.56
PPE35 2169063 p.Met517Thr missense_variant 0.67
PPE35 2169065 p.Ala516Thr missense_variant 0.56
PPE35 2169068 c.1545G>T synonymous_variant 0.56
PPE35 2169200 c.1413G>T synonymous_variant 0.61
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.24
Rv1979c 2222308 p.Asp286Gly missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714871 c.462G>T synonymous_variant 0.93
ahpC 2726051 c.-142G>A upstream_gene_variant 0.91
Rv2752c 3064749 c.1443T>A synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.83
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.92
fprA 3475159 p.Asn385Asp missense_variant 0.83
clpC1 4040517 p.Val63Ala missense_variant 0.96
embC 4240671 p.Thr270Ile missense_variant 0.98
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 0.83
aftB 4268468 c.369G>C synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.45
aftB 4269606 c.-770T>C upstream_gene_variant 0.75
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 0.89
whiB6 4338203 p.Arg107Cys missense_variant 0.95
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 0.9