TB-Profiler result

Run: SRR6650302
Summary

Run ID: SRR6650302

Sample name:

Date: 15-08-2023 08:21:21

Number of reads: 935077

Percentage reads mapped: 99.62

Strain: lineage3

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 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
gyrA 6889 c.-413G>T upstream_gene_variant 0.15
gyrB 6913 p.Asn558Lys missense_variant 0.18
gyrA 6922 c.-380G>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.25
fgd1 490756 c.-27T>G upstream_gene_variant 0.22
fgd1 490759 c.-24A>T upstream_gene_variant 0.22
fgd1 490761 c.-22G>T upstream_gene_variant 0.22
fgd1 490769 c.-14A>G upstream_gene_variant 0.2
fgd1 490771 c.-12T>G upstream_gene_variant 0.2
fgd1 490780 c.-3C>A upstream_gene_variant 0.2
fgd1 490787 p.Ala2Gly missense_variant 0.18
fgd1 490979 p.Asn66Thr missense_variant 0.2
fgd1 491014 p.Thr78Pro missense_variant 0.28
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575165 c.-183C>T upstream_gene_variant 0.25
mshA 575176 c.-172T>G upstream_gene_variant 0.18
mshA 576723 p.Val459Gly missense_variant 0.3
ccsA 620537 p.Val216Gly missense_variant 0.2
ccsA 620551 p.Asp221His missense_variant 0.25
ccsA 620558 p.Gln223Pro missense_variant 0.25
ccsA 620584 p.Thr232Ala missense_variant 0.22
ccsA 620748 c.858T>G synonymous_variant 0.24
ccsA 620752 p.Arg288Gly missense_variant 0.24
ccsA 620756 p.Asp289Gly missense_variant 0.44
ccsA 620759 p.Arg290Pro missense_variant 0.16
ccsA 620761 p.Lys291Gln missense_variant 0.15
ccsA 620770 p.Trp294Arg missense_variant 0.2
ccsA 620773 p.Ile295Val missense_variant 0.19
rpoB 759620 c.-187A>C upstream_gene_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775603 p.Thr960Pro missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.27
fbiC 1303016 p.Val29Gly missense_variant 0.33
fbiC 1303031 p.Arg34Pro missense_variant 0.14
fbiC 1303050 p.Asn40Lys missense_variant 0.17
fbiC 1303055 p.Asp42Gly missense_variant 0.17
fbiC 1303061 p.Ala44Gly missense_variant 0.2
fbiC 1303064 p.Ala45Gly missense_variant 0.2
fbiC 1304136 c.1206C>G synonymous_variant 0.18
fbiC 1304146 p.Ile406Val missense_variant 0.18
Rv1258c 1407081 p.Ala87Gly missense_variant 0.17
Rv1258c 1407084 p.Val86Gly missense_variant 0.25
atpE 1461086 c.42A>G synonymous_variant 0.17
atpE 1461119 c.75T>G synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473640 n.-18C>T upstream_gene_variant 1.0
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.25
rrl 1475252 n.1595C>G non_coding_transcript_exon_variant 1.0
fabG1 1673690 p.Val84Gly missense_variant 0.17
fabG1 1674076 p.Thr213Pro missense_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918010 p.Ala24Gly missense_variant 0.27
tlyA 1918052 p.Pro38Arg missense_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.25
ndh 2103235 c.-193C>G upstream_gene_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169299 p.Asn438Lys missense_variant 0.14
PPE35 2169308 c.1305C>G synonymous_variant 0.15
PPE35 2169314 p.Asn433Lys missense_variant 0.2
PPE35 2169854 c.759T>G synonymous_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288951 c.291T>G synonymous_variant 0.23
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.32
kasA 2518151 p.Ser13Arg missense_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726261 c.69G>T synonymous_variant 0.13
ahpC 2726286 p.Gly32Arg missense_variant 0.17
ahpC 2726338 p.Val49Gly missense_variant 0.25
ahpC 2726341 p.Val50Gly missense_variant 0.22
ahpC 2726345 c.153C>T synonymous_variant 0.21
ahpC 2726350 p.Trp53Leu missense_variant 0.22
ahpC 2726360 p.Asp56Glu missense_variant 0.15
pepQ 2859414 c.1005T>G synonymous_variant 0.22
pepQ 2859438 c.981T>G synonymous_variant 0.24
pepQ 2859904 p.Val172Gly missense_variant 0.2
ribD 2987316 p.Ala160Pro missense_variant 0.17
ribD 2987320 p.Glu161Gly missense_variant 0.15
ribD 2987323 p.Val162Gly missense_variant 0.15
Rv2752c 3065226 c.966G>A synonymous_variant 1.0
thyA 3074641 c.-170C>T upstream_gene_variant 0.17
thyA 3074648 c.-177T>G upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448759 p.Ala86Pro missense_variant 0.19
Rv3083 3448765 p.Thr88Pro missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568401 c.279G>C stop_lost&splice_region_variant 0.22
whiB7 3568419 c.261C>A synonymous_variant 0.23
alr 3841230 p.Val64Gly missense_variant 0.18
clpC1 4038163 p.Arg848Gly missense_variant 0.18
clpC1 4038165 p.Ala847Gly missense_variant 0.18
clpC1 4039468 p.Arg413Cys missense_variant 0.22
clpC1 4039484 c.1221T>G synonymous_variant 0.3
clpC1 4039890 p.Val272Gly missense_variant 0.22
embC 4239973 c.111T>G synonymous_variant 0.15
embC 4241412 p.Ile517Thr missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242212 p.Ala784Pro missense_variant 0.17
embC 4242220 c.2358A>C synonymous_variant 0.21
embC 4242390 p.Leu843Arg missense_variant 0.18
embC 4242393 p.Asp844Ala missense_variant 0.18
embA 4242406 c.-827A>C upstream_gene_variant 0.25
embC 4242414 p.Leu851Arg missense_variant 0.17
embC 4242422 p.Trp854Gly missense_variant 0.18
embC 4242425 p.Arg855Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242908 p.Phe1016Val missense_variant 0.17
embA 4243350 p.Thr40Pro missense_variant 0.21
embA 4243372 p.Gln47Arg missense_variant 0.14
embA 4243380 p.Thr50Pro missense_variant 0.19
embA 4244748 p.Thr506Pro missense_variant 0.16
embB 4247616 p.Glu368Gly missense_variant 0.18
embB 4248725 p.Ser738Ala missense_variant 0.18
embB 4249293 p.Lys927Arg missense_variant 0.14
embB 4249296 p.Ala928Gly missense_variant 0.21
embB 4249298 p.Trp929Gly missense_variant 0.21
embB 4249305 p.Asn931Thr missense_variant 0.23
embB 4249322 p.Ala937Lys missense_variant 0.27
embB 4249329 p.Met939Thr missense_variant 0.18
embB 4249394 p.Ile961Phe missense_variant 0.14
aftB 4268776 p.Ser21Gly missense_variant 0.18
ubiA 4269514 p.Val107Gly missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0