TB-Profiler result

Run: ERR2245357
Summary

Run ID: ERR2245357

Sample name:

Date: 31-03-2023 17:39:10

Number of reads: 1851596

Percentage reads mapped: 99.1

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
lineage3.1.1 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 5309 p.Glu24Lys missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7459 p.Arg53Leu missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8216 p.Gln305His missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9431 c.2130G>T synonymous_variant 0.29
fgd1 491049 c.267T>A synonymous_variant 0.33
fgd1 491605 p.Leu275Met missense_variant 0.25
fgd1 491686 p.Thr302Pro missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575752 c.405G>T synonymous_variant 0.5
mshA 575847 p.Asp167Ala missense_variant 0.6
ccsA 620371 p.Ala161Ser missense_variant 0.4
ccsA 620704 p.Trp272Arg missense_variant 0.4
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759841 p.Ser12Asn missense_variant 0.33
rpoB 761885 c.2079T>G synonymous_variant 0.43
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763384 c.15C>T synonymous_variant 0.13
rpoC 763934 p.Ala189Pro missense_variant 0.25
rpoC 765414 p.Pro682Gln missense_variant 0.29
rpoC 766155 p.Ala929Val missense_variant 0.33
rpoC 766914 p.Asp1182Ala missense_variant 0.29
rpoC 766923 p.Glu1185Val missense_variant 0.29
rpoC 767174 p.Asn1269Tyr missense_variant 0.67
mmpL5 775826 c.2655G>A synonymous_variant 1.0
mmpL5 776674 p.Val603Leu missense_variant 0.25
mmpL5 776818 p.Ile555Phe missense_variant 0.13
mmpL5 777419 c.1062C>A synonymous_variant 0.29
mmpS5 778661 p.Asp82Ala missense_variant 0.33
mmpL5 778992 c.-512C>A upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781896 p.Ala113Thr missense_variant 0.12
fbiC 1303599 p.Phe223Leu missense_variant 0.4
fbiC 1304044 p.Pro372Thr missense_variant 0.5
fbiC 1305438 c.2508C>T synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473406 n.-252A>T upstream_gene_variant 0.18
fabG1 1673191 c.-249C>A upstream_gene_variant 0.22
fabG1 1673335 c.-105C>G upstream_gene_variant 0.17
inhA 1674222 c.21C>A synonymous_variant 0.29
inhA 1674620 p.Pro140His missense_variant 0.29
rpsA 1833559 c.18C>A synonymous_variant 0.2
rpsA 1833930 p.Val130Gly missense_variant 0.29
rpsA 1834267 p.Trp242Cys missense_variant 0.4
rpsA 1834982 p.Ala481Thr missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102875 c.168C>T synonymous_variant 0.25
ndh 2102979 p.Ser22Ala missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155509 c.603A>G synonymous_variant 0.29
katG 2155526 p.Val196Phe missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169701 p.Asn304Lys missense_variant 0.12
PPE35 2170040 c.573G>T synonymous_variant 0.4
PPE35 2170461 p.Gly51Glu missense_variant 1.0
PPE35 2170667 c.-55C>A upstream_gene_variant 0.17
Rv1979c 2222702 p.Gly155Ser missense_variant 0.29
Rv1979c 2222778 c.387C>T synonymous_variant 0.15
Rv1979c 2223021 c.144G>T synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290047 c.-806G>T upstream_gene_variant 0.29
kasA 2518251 p.Leu46Pro missense_variant 0.11
kasA 2518675 p.Met187Ile missense_variant 0.67
kasA 2518695 p.Val194Gly missense_variant 0.67
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859463 p.Gly319Val missense_variant 0.22
ribD 2987084 c.246G>A synonymous_variant 0.5
ribD 2987090 c.252C>A synonymous_variant 0.5
Rv2752c 3064566 c.1626G>C synonymous_variant 0.38
Rv2752c 3064628 p.Asn522Tyr missense_variant 0.33
Rv2752c 3064963 p.Ala410Val missense_variant 0.33
Rv2752c 3065669 p.Gln175Lys missense_variant 0.4
thyA 3074444 p.Phe10Val missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087096 p.Thr93Pro missense_variant 1.0
ald 3087695 p.Asp292Glu missense_variant 0.33
fbiD 3338986 c.-132G>A upstream_gene_variant 0.29
Rv3083 3449440 p.Ala313Ser missense_variant 0.33
Rv3083 3449670 c.1167C>A synonymous_variant 0.22
fprA 3473936 c.-71A>C upstream_gene_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474230 p.Arg75Leu missense_variant 0.5
fprA 3474607 p.Gly201Ser missense_variant 0.5
fprA 3474643 p.Arg213Ser missense_variant 0.43
fbiB 3642413 c.879G>T synonymous_variant 0.2
rpoA 3878120 p.Asp130Asn missense_variant 1.0
rpoA 3878490 c.18C>G synonymous_variant 0.4
clpC1 4038755 c.1950G>T synonymous_variant 0.25
clpC1 4040144 c.561G>C synonymous_variant 0.18
clpC1 4040219 c.486C>T synonymous_variant 0.17
clpC1 4040803 c.-99G>T upstream_gene_variant 0.18
clpC1 4040832 c.-128G>T upstream_gene_variant 0.22
clpC1 4040887 c.-183C>A upstream_gene_variant 0.33
embC 4240089 p.Gly76Val missense_variant 0.33
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240763 p.Ala301Ser missense_variant 0.18
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241940 p.Pro693Gln missense_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242763 c.-470G>T upstream_gene_variant 0.4
embA 4243171 c.-62C>A upstream_gene_variant 0.13
embA 4244126 c.894C>A synonymous_variant 0.4
embA 4244156 c.924A>T synonymous_variant 0.33
embA 4244183 c.951G>T synonymous_variant 0.4
embB 4246010 c.-504G>A upstream_gene_variant 0.33
embB 4248327 p.Ala605Glu missense_variant 0.4
embB 4248628 c.2115C>G synonymous_variant 0.4
embB 4248879 p.Thr789Lys missense_variant 0.25
aftB 4267962 p.Pro292His missense_variant 0.33
aftB 4268619 p.Val73Gly missense_variant 0.3
aftB 4268634 p.Tyr68Phe missense_variant 0.33
ethA 4327336 p.Asp46Glu missense_variant 0.29
ethR 4327650 p.Glu34Asp missense_variant 0.4
ethR 4328010 p.Asp154Glu missense_variant 0.2
ethR 4328060 p.Leu171Gln missense_variant 0.33
whiB6 4338380 p.Glu48* stop_gained 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0