TB-Profiler result

Run: ERR2245348
Summary

Run ID: ERR2245348

Sample name:

Date: 31-03-2023 17:39:02

Number of reads: 2025871

Percentage reads mapped: 87.2

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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 6290 c.1054dupG frameshift_variant 0.2
gyrA 6556 c.-746C>T upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7623 p.Pro108Ser missense_variant 0.15
gyrA 8414 c.1113C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9383 c.2082T>G synonymous_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576676 c.1329T>G synonymous_variant 0.18
ccsA 620711 p.Val274Gly missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759986 c.180T>C synonymous_variant 0.1
rpoB 760573 c.769dupG frameshift_variant 0.13
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoB 762708 p.Thr968Pro missense_variant 0.27
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764246 p.Leu293Ile missense_variant 0.29
rpoC 766326 p.Gly986Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777191 c.1290C>A synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303396 p.Arg156Gly missense_variant 0.12
fbiC 1303670 p.Asp247Ala missense_variant 0.27
Rv1258c 1406248 p.Leu365Val missense_variant 0.15
embR 1416896 p.Asp151Gly missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473635 n.-23A>T upstream_gene_variant 0.29
rrl 1475666 n.2009T>A non_coding_transcript_exon_variant 0.4
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.25
fabG1 1673636 p.Asp66Ala missense_variant 0.21
rpsA 1833883 c.342C>G synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155050 c.1062C>T synonymous_variant 0.2
katG 2156297 c.-186T>G upstream_gene_variant 0.17
PPE35 2167916 c.2696delT frameshift_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169049 p.Ile522Phe missense_variant 0.18
PPE35 2169063 p.Met517Lys missense_variant 0.38
PPE35 2170082 c.531T>G synonymous_variant 0.29
PPE35 2170119 p.Leu165Arg missense_variant 0.17
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2222393 p.Ile258Phe missense_variant 0.13
Rv1979c 2222657 p.Lys170Glu missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289075 p.Asp56Ala missense_variant 0.19
pncA 2289301 c.-60T>A upstream_gene_variant 0.12
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519039 p.Asn309Asp missense_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2986994 c.156C>T synonymous_variant 0.12
Rv2752c 3065092 c.1099delC frameshift_variant 0.12
Rv2752c 3065339 p.Asp285Asn missense_variant 0.14
Rv2752c 3065883 c.309C>A synonymous_variant 0.29
thyX 3067962 c.-17G>T upstream_gene_variant 0.12
thyA 3074204 p.Leu90Ile missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087861 p.Gly348Trp missense_variant 0.18
fbiD 3339472 p.Ala119Ser missense_variant 0.12
Rv3083 3449587 p.Gly362Ser missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474046 p.Ser14Ala missense_variant 0.18
whiB7 3568489 p.Gly64Ala missense_variant 0.12
Rv3236c 3612593 p.Asp175Val missense_variant 0.15
fbiB 3641937 p.Gly135Arg missense_variant 0.11
fbiB 3642839 c.1305G>A synonymous_variant 0.13
fbiB 3642857 c.1323C>A synonymous_variant 0.12
rpoA 3878641 c.-134C>G upstream_gene_variant 0.67
panD 4044235 p.Thr16Asn missense_variant 0.12
embC 4239903 c.42dupA frameshift_variant 0.14
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242683 p.Thr941Ser missense_variant 0.2
embA 4244550 p.Ala440Thr missense_variant 0.17
embA 4244745 p.Leu505Val missense_variant 0.25
embA 4245583 p.Asp784Val missense_variant 0.13
embA 4246206 p.Pro992Ser missense_variant 0.14
embB 4249134 p.Leu874Pro missense_variant 0.14
aftB 4268619 p.Val73Gly missense_variant 0.29
ubiA 4269354 c.479delG frameshift_variant 0.18
ethA 4328454 c.-982delG upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407832 p.Val124Ala missense_variant 0.12