TB-Profiler result

Run: SRR19428614
Summary

Run ID: SRR19428614

Sample name:

Date: 03-04-2023 21:42:17

Number of reads: 528341

Percentage reads mapped: 95.25

Strain: lineage3.1.1

Drug-resistance: HR-TB

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
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
katG 2155129 p.Trp328Leu missense_variant 0.17 isoniazid
gid 4407832 c.370delG frameshift_variant 1.0 streptomycin
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 7175 p.Glu646* stop_gained 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7587 p.Leu96Met missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491346 c.564C>T synonymous_variant 0.15
fgd1 491376 p.Lys198Asn missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619828 c.-63G>T upstream_gene_variant 0.17
ccsA 619837 c.-54G>T upstream_gene_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760507 p.Ala234Glu missense_variant 0.14
rpoB 760625 c.819C>A synonymous_variant 0.17
rpoB 761969 p.Glu721Asp missense_variant 0.16
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762857 c.-513C>A upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 0.15
rpoC 766296 p.Ala976Glu missense_variant 0.15
rpoC 766901 p.Gly1178Cys missense_variant 0.17
rpoC 766944 p.Arg1192Pro missense_variant 0.12
rpoC 767053 c.3684G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775894 p.His863Asn missense_variant 0.19
mmpL5 775919 c.2562G>T synonymous_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776539 p.Met648Val missense_variant 0.12
mmpL5 776988 p.Pro498Gln missense_variant 0.25
mmpL5 777025 c.1456C>A synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800663 c.-146G>T upstream_gene_variant 0.2
rplC 801123 c.315C>A synonymous_variant 0.15
fbiC 1304192 p.Ala421Glu missense_variant 0.13
fbiC 1304433 c.1503G>T synonymous_variant 0.15
embR 1417196 p.Gly51Val missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472633 n.788C>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.18
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.18
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.18
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.18
rrs 1472679 n.834_835insAC non_coding_transcript_exon_variant 0.18
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.16
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.15
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.15
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.14
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.3
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.3
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.3
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.33
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.29
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.26
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.24
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.19
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.21
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.12
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.12
rrs 1472842 n.997G>T non_coding_transcript_exon_variant 0.14
rrl 1473811 n.154C>A non_coding_transcript_exon_variant 0.21
rrl 1473942 n.285G>T non_coding_transcript_exon_variant 0.17
rrl 1474543 n.886G>T non_coding_transcript_exon_variant 0.21
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.12
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.12
fabG1 1673324 c.-116G>T upstream_gene_variant 0.15
fabG1 1673411 c.-29C>A upstream_gene_variant 0.15
fabG1 1674158 p.Asp240Gly missense_variant 0.12
inhA 1674363 c.162G>T synonymous_variant 0.17
inhA 1674448 p.Gly83Trp missense_variant 0.29
inhA 1674469 p.Gly90Trp missense_variant 0.22
inhA 1674504 c.303C>A synonymous_variant 0.2
rpsA 1833443 c.-99C>A upstream_gene_variant 0.17
rpsA 1834782 p.Trp414Leu missense_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101827 p.Gly406Trp missense_variant 0.2
katG 2154578 p.Gly512Trp missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155062 c.1050T>C synonymous_variant 0.12
katG 2155817 p.Gly99Trp missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168299 p.Pro772Thr missense_variant 0.18
PPE35 2168372 c.2241G>A synonymous_variant 0.17
PPE35 2170269 p.Ser115Tyr missense_variant 0.2
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2221755 c.1410C>A synonymous_variant 0.16
Rv1979c 2223218 c.-54C>A upstream_gene_variant 0.27
Rv1979c 2223235 c.-71G>T upstream_gene_variant 0.15
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 2290005 c.-764G>T upstream_gene_variant 0.18
kasA 2518421 c.308delT frameshift_variant 0.11
kasA 2518484 p.Glu124Lys missense_variant 0.17
kasA 2518568 p.Ala152Ser missense_variant 0.13
kasA 2518645 c.531G>T synonymous_variant 0.15
eis 2714765 p.Leu190Met missense_variant 0.15
ahpC 2725914 c.-279G>T upstream_gene_variant 0.22
ahpC 2725926 c.-266delG upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746665 p.Phe312Leu missense_variant 0.11
pepQ 2859403 p.Glu339Gly missense_variant 0.11
pepQ 2859462 c.957C>A synonymous_variant 0.17
Rv2752c 3065418 c.774A>G synonymous_variant 0.11
Rv2752c 3065929 p.Gly88Val missense_variant 0.13
thyX 3067610 p.Lys112Asn missense_variant 0.21
thyX 3067961 c.-17delG upstream_gene_variant 0.11
thyA 3074396 p.Thr26Pro missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087913 p.Glu365Ala missense_variant 0.18
fbiD 3338919 c.-199C>A upstream_gene_variant 0.17
fbiD 3339379 p.Asp88Tyr missense_variant 0.17
Rv3083 3449100 c.597C>G synonymous_variant 0.22
Rv3083 3449105 p.Pro201His missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568649 p.Pro11Thr missense_variant 0.14
Rv3236c 3612041 p.Val359Ala missense_variant 0.25
Rv3236c 3612093 p.Gly342Trp missense_variant 0.17
Rv3236c 3612177 c.940C>A synonymous_variant 0.22
fbiA 3641108 p.Gly189Val missense_variant 0.18
fbiA 3641176 p.Ala212Ser missense_variant 0.18
fbiA 3641332 p.Gly264Trp missense_variant 0.17
fbiB 3642024 p.Ala164Thr missense_variant 0.22
fbiB 3642066 p.Gly178Ser missense_variant 0.17
alr 3841272 p.Arg50Leu missense_variant 0.17
clpC1 4038258 p.Ala816Val missense_variant 0.15
clpC1 4038342 p.Lys788Arg missense_variant 0.18
clpC1 4040394 p.Gly104Val missense_variant 0.13
panD 4044161 c.120delA frameshift_variant 0.15
embC 4239885 p.Pro8His missense_variant 0.14
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241793 p.Ser644Tyr missense_variant 0.16
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242622 c.-611C>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243293 p.Gly21* stop_gained 0.2
embA 4243319 c.87C>A synonymous_variant 0.2
embA 4243426 p.Gly65Val missense_variant 0.25
embA 4243566 p.Asp112Tyr missense_variant 0.17
embA 4243960 p.Arg243Leu missense_variant 0.16
embA 4244557 p.Arg442Met missense_variant 0.13
embA 4244780 c.1548C>A synonymous_variant 0.2
embA 4245404 c.2172C>A synonymous_variant 0.15
embA 4245461 c.2229C>G synonymous_variant 1.0
embA 4245516 p.Gly762* stop_gained 0.2
embA 4246483 p.Trp1084Leu missense_variant 0.14
embB 4249125 p.Gly871Val missense_variant 0.17
embB 4249413 p.Arg967Leu missense_variant 0.14
embB 4249730 p.Ala1073Ser missense_variant 0.17
ubiA 4269521 p.Val105Met missense_variant 0.15
ubiA 4269714 p.Leu40Phe missense_variant 0.18
ubiA 4270004 c.-171G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0