TB-Profiler result

Run: SRR5535683
Summary

Run ID: SRR5535683

Sample name:

Date: 04-04-2023 10:37:39

Number of reads: 3121400

Percentage reads mapped: 99.08

Strain: lineage1.2.1.2.1

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
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.99
lineage1.2.1.2 Indo-Oceanic NA RD239 0.98
lineage1.2.1.2.1 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 6112 p.Met291Ile missense_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 8802 p.Ala501Tyr missense_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
rpoB 760783 p.Thr326Lys missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763603 c.234C>T synonymous_variant 0.12
rpoC 763620 p.Arg84Leu missense_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 766973 p.Ala1202Ser missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777869 c.612G>T synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406990 c.351C>G synonymous_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471788 n.-58G>T upstream_gene_variant 0.14
rrl 1473630 n.-28G>T upstream_gene_variant 0.14
rrl 1474340 n.683C>A non_coding_transcript_exon_variant 0.29
rrl 1474537 n.880G>T non_coding_transcript_exon_variant 0.33
rrl 1475916 n.2259C>A non_coding_transcript_exon_variant 0.17
rrl 1476021 n.2364G>T non_coding_transcript_exon_variant 0.29
rrl 1476610 n.2953C>A non_coding_transcript_exon_variant 0.33
rrl 1476763 n.3106G>C non_coding_transcript_exon_variant 0.17
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101824 p.Phe407Val missense_variant 0.17
ndh 2102085 p.Val320Leu missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.11
PPE35 2169720 p.Gly298Val missense_variant 0.15
PPE35 2170445 c.167_168insAGGC frameshift_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289524 c.-283C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746162 c.1437G>T synonymous_variant 0.14
pepQ 2859731 p.His230Asn missense_variant 0.18
pepQ 2859747 c.672C>A synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 0.94
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449116 p.Ala205Ser missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474957 c.951G>T synonymous_variant 0.18
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612304 c.805_812delTTGTTCGC frameshift_variant 0.2
Rv3236c 3612529 p.Phe196Leu missense_variant 0.12
Rv3236c 3612999 p.Gly40Cys missense_variant 0.14
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
clpC1 4038262 p.Asp815Tyr missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243165 c.-68A>G upstream_gene_variant 0.13
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.97
aftB 4268626 p.Gly71Cys missense_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln 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 4407873 c.330G>T synonymous_variant 1.0