TB-Profiler result

Run: ERR3256195
Summary

Run ID: ERR3256195

Sample name:

Date: 01-04-2023 00:57:24

Number of reads: 214921

Percentage reads mapped: 99.44

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 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 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 5332 c.93C>T synonymous_variant 0.29
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6553 c.-749G>A upstream_gene_variant 0.25
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 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 761725 p.Glu640Gly missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763937 p.Lys190* stop_gained 0.17
rpoC 765611 p.His748Tyr missense_variant 0.12
rpoC 765750 c.2386_2388delGAC conservative_inframe_deletion 0.14
rpoC 765768 p.Ile800Thr missense_variant 0.13
rpoC 766403 p.Met1012Val missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776598 p.Asp628Val missense_variant 0.15
mmpL5 777208 p.Leu425Ile missense_variant 0.13
mmpL5 777813 p.Tyr223Cys missense_variant 0.1
mmpL5 778134 p.Leu116Pro missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781442 c.-118C>T upstream_gene_variant 0.2
rpsL 781539 c.-21C>T upstream_gene_variant 0.17
fbiC 1303376 p.Asp149Gly missense_variant 0.1
fbiC 1304924 p.Pro665Arg missense_variant 0.17
fbiC 1304956 p.Val676Ile missense_variant 0.15
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
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
rrl 1474484 n.827C>A non_coding_transcript_exon_variant 0.18
inhA 1673458 c.-744G>A upstream_gene_variant 0.18
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102365 c.678A>G synonymous_variant 0.33
ndh 2103003 p.Arg14Trp missense_variant 0.2
katG 2154392 p.Ala574Thr missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155047 c.1065C>T synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168010 p.Ser868Ile missense_variant 0.14
PPE35 2169056 c.1556delC frameshift_variant 0.17
PPE35 2169231 p.Thr461Met missense_variant 0.2
Rv1979c 2221866 p.Asp433Glu missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222401 c.762_763delAG frameshift_variant 0.2
Rv1979c 2222891 p.Ile92Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G 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 2747078 c.520delG frameshift_variant 0.14
pepQ 2859348 p.Gln357His missense_variant 0.15
pepQ 2859997 p.Ala141Val missense_variant 0.17
ribD 2986820 c.-19A>T upstream_gene_variant 0.17
Rv2752c 3066010 p.Leu61Pro missense_variant 0.11
Rv2752c 3066039 c.153C>T synonymous_variant 0.13
Rv2752c 3066260 c.-69T>A upstream_gene_variant 0.18
thyX 3067755 p.Ile64Thr missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087389 p.Met190Ile missense_variant 0.15
fbiD 3339267 c.150G>T synonymous_variant 0.18
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448469 c.-35A>T upstream_gene_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449474 p.Phe324Tyr missense_variant 0.2
Rv3083 3449593 p.Glu364Lys missense_variant 0.18
Rv3083 3449652 c.1149T>C synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474705 c.699T>C synonymous_variant 0.29
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3640638 c.-897T>C upstream_gene_variant 0.33
fbiB 3642213 p.Ser227Thr missense_variant 0.2
fbiB 3642759 p.Arg409Cys missense_variant 1.0
clpC1 4038513 p.Val731Asp missense_variant 0.12
clpC1 4040189 c.516C>T synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044036 c.246G>A synonymous_variant 0.15
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 4243541 c.312delG frameshift_variant 0.25
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245772 p.Asn847Ser missense_variant 0.25
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267674 p.Trp388* stop_gained 0.22
aftB 4268587 p.Leu84Met missense_variant 0.22
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
ethA 4326196 c.1278C>A synonymous_variant 0.11
ethA 4326368 p.Tyr369Cys missense_variant 0.13
ethR 4326856 c.-693C>T upstream_gene_variant 0.17
ethA 4326867 p.Thr203Ser missense_variant 0.17
whiB6 4338348 c.174C>T synonymous_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
gid 4408226 c.-24C>T upstream_gene_variant 1.0