TB-Profiler result

Run: SRR7517724
Summary

Run ID: SRR7517724

Sample name:

Date: 04-04-2023 19:33:54

Number of reads: 148539

Percentage reads mapped: 98.8

Strain: lineage4;lineage2

Drug-resistance: HR-TB

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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
lineage2 East-Asian Beijing RD105 0.06
lineage4 Euro-American LAM;T;S;X;H None 0.92
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 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
ethA 4326707 p.Trp256* stop_gained 1.0 ethionamide
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 5470 c.231C>A synonymous_variant 0.5
gyrB 5497 c.258C>A synonymous_variant 0.4
gyrA 9040 p.Lys580Met missense_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576431 p.Ala362Ser missense_variant 0.17
ccsA 620178 c.288G>T synonymous_variant 0.29
ccsA 620238 c.348G>T synonymous_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764773 p.Asn468Lys missense_variant 0.2
rpoC 764845 c.1476C>A synonymous_variant 0.33
rpoC 765608 p.Asp747Tyr missense_variant 1.0
mmpL5 776126 p.Cys785* stop_gained 0.67
mmpL5 776162 c.2319C>A synonymous_variant 0.67
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776300 p.Met727Ile missense_variant 0.67
mmpL5 776446 p.Ala679Ser missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801254 p.Gly149Val missense_variant 0.67
rplC 801284 p.Arg159Leu missense_variant 0.67
fbiC 1303209 c.279G>T synonymous_variant 0.4
Rv1258c 1406315 c.1026G>A synonymous_variant 0.4
Rv1258c 1407350 c.-10C>A upstream_gene_variant 0.67
embR 1416635 p.Asp238Val missense_variant 0.67
embR 1416778 c.570G>T synonymous_variant 0.33
rrl 1476415 n.2758C>A non_coding_transcript_exon_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834946 p.Gln469* stop_gained 0.5
tlyA 1917916 c.-24C>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918081 p.Asp48Tyr missense_variant 0.25
tlyA 1918152 c.213C>A synonymous_variant 0.33
tlyA 1918384 p.Asp149Tyr missense_variant 0.33
ndh 2103065 c.-23G>T upstream_gene_variant 1.0
katG 2153952 p.Phe720Leu missense_variant 0.67
katG 2154488 p.Asp542Tyr missense_variant 1.0
katG 2154617 p.Leu499Met missense_variant 1.0
katG 2155926 p.Phe62Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
kasA 2518451 p.Gly113Cys missense_variant 1.0
eis 2714988 c.345C>A synonymous_variant 1.0
ahpC 2726085 c.-108G>T upstream_gene_variant 0.67
ahpC 2726129 c.-64G>T upstream_gene_variant 1.0
folC 2746445 p.Lys385Arg missense_variant 0.25
folC 2747532 p.Glu23* stop_gained 0.5
folC 2747684 c.-86G>T upstream_gene_variant 0.4
pepQ 2859720 p.Met233Ile missense_variant 0.5
pepQ 2859910 p.Arg170Leu missense_variant 0.4
pepQ 2860487 c.-69G>T upstream_gene_variant 0.33
Rv2752c 3064951 p.Gly414Val missense_variant 0.67
thyX 3068000 c.-55G>T upstream_gene_variant 1.0
thyX 3068150 c.-205C>A upstream_gene_variant 1.0
thyA 3073798 p.Arg225Leu missense_variant 0.67
fbiD 3339364 p.Pro83Thr missense_variant 0.5
fbiD 3339635 p.Ser173* stop_gained 0.2
fbiD 3339679 p.Asp188Tyr missense_variant 0.22
Rv3083 3449538 c.1035G>T synonymous_variant 0.5
fprA 3474791 p.Pro262Gln missense_variant 0.25
fprA 3474901 p.Ser299Gly missense_variant 0.33
whiB7 3568758 c.-79C>T upstream_gene_variant 0.5
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641862 p.Gly110* stop_gained 0.33
fbiB 3642173 c.639G>A synonymous_variant 0.29
alr 3840376 p.Asp349Tyr missense_variant 0.29
alr 3841160 c.261C>A synonymous_variant 0.2
alr 3841164 p.Ala86Glu missense_variant 0.2
alr 3841204 p.Gly73Cys missense_variant 0.29
alr 3841245 p.Ala59Val missense_variant 0.5
rpoA 3877676 p.Arg278Ser missense_variant 0.4
ddn 3986988 p.Leu49Met missense_variant 0.67
clpC1 4039527 p.Arg393Leu missense_variant 0.67
clpC1 4040069 c.636G>T synonymous_variant 1.0
clpC1 4040308 c.397C>A synonymous_variant 0.67
embA 4242637 c.-596C>A upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
aftB 4267785 p.Gly351Val missense_variant 0.5
aftB 4267980 p.Arg286Leu missense_variant 0.4
aftB 4268318 c.519C>A synonymous_variant 0.18
aftB 4268364 p.Trp158Leu missense_variant 0.29
aftB 4268825 c.12C>T synonymous_variant 0.4
aftB 4269492 c.-656G>A upstream_gene_variant 0.4
aftB 4269678 c.-842C>A upstream_gene_variant 0.5
whiB6 4338232 p.Ser97Tyr missense_variant 0.33
whiB6 4338371 p.Thr51Pro missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408285 c.-83C>A upstream_gene_variant 1.0