TB-Profiler result

Run: SRR4035733
Summary

Run ID: SRR4035733

Sample name:

Date: 04-04-2023 07:15:56

Number of reads: 839718

Percentage reads mapped: 99.42

Strain: lineage4.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.97
lineage4.1.2 Euro-American T;H None 0.98
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 5815 c.576C>T synonymous_variant 0.12
gyrA 6973 c.-329G>C upstream_gene_variant 0.15
gyrB 6980 p.Ala581Thr missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7624 p.Pro108Leu missense_variant 0.2
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9147 p.Gly616Ser missense_variant 0.18
gyrA 9260 c.1959G>T synonymous_variant 0.2
gyrA 9281 c.1980C>G synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9307 p.Asp669Gly missense_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491643 c.861G>A synonymous_variant 0.17
mshA 575798 p.Val151Met missense_variant 0.13
mshA 576512 c.1165C>T synonymous_variant 0.2
ccsA 620828 p.Val313Glu missense_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762684 p.Ala960Thr missense_variant 0.15
rpoC 763703 p.Ser112Ala missense_variant 0.13
rpoC 763708 c.339G>A synonymous_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764798 p.Glu477Lys missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765387 p.Phe673Tyr missense_variant 0.17
rpoC 766078 p.Glu903Asp missense_variant 0.17
rpoC 766338 p.Asp990Gly missense_variant 0.18
rpoC 766479 p.Ala1037Val missense_variant 0.15
rpoC 766488 p.Pro1040Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776049 p.Ser811Leu missense_variant 0.17
mmpL5 776472 p.Gln670Arg missense_variant 0.11
mmpL5 777320 c.1161C>G synonymous_variant 0.86
mmpL5 777844 p.Thr213Ala missense_variant 0.11
mmpL5 777928 p.Tyr185Asn missense_variant 0.12
mmpR5 779122 p.Val45Met missense_variant 0.18
mmpL5 779139 c.-659C>T upstream_gene_variant 0.25
mmpR5 779366 p.Gly126Asp missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303720 p.Gly264Ser missense_variant 0.14
fbiC 1303741 p.Ala271Thr missense_variant 0.13
fbiC 1304348 p.Trp473Ser missense_variant 0.14
fbiC 1304540 p.Arg537His missense_variant 0.14
fbiC 1304901 c.1971C>T synonymous_variant 0.13
fbiC 1304946 c.2016G>A synonymous_variant 0.13
Rv1258c 1406917 p.Ile142Phe missense_variant 0.12
embR 1416184 c.1164G>C synonymous_variant 0.11
embR 1416713 p.Ile212Asn missense_variant 0.2
atpE 1460878 c.-167C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472196 n.351C>G non_coding_transcript_exon_variant 0.12
rrs 1472436 n.591G>A non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>G non_coding_transcript_exon_variant 0.15
rrl 1473910 n.253A>G non_coding_transcript_exon_variant 0.13
rrl 1475437 n.1780G>A non_coding_transcript_exon_variant 0.17
rrl 1475455 n.1798C>T non_coding_transcript_exon_variant 0.13
rrl 1476663 n.3006C>G non_coding_transcript_exon_variant 0.11
fabG1 1673319 c.-121A>T upstream_gene_variant 0.14
fabG1 1673447 p.Ala3Val missense_variant 0.18
inhA 1674153 c.-49G>T upstream_gene_variant 0.13
rpsA 1833910 c.369C>T synonymous_variant 0.14
rpsA 1834228 c.687C>G synonymous_variant 0.12
rpsA 1834248 p.His236Pro missense_variant 0.14
rpsA 1834734 p.Ala398Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918379 p.Arg147His missense_variant 0.18
ndh 2101936 c.1107G>A synonymous_variant 0.14
ndh 2102913 p.Ala44Ser missense_variant 0.2
ndh 2103124 c.-82T>C upstream_gene_variant 0.17
katG 2154734 p.Ser460Gly missense_variant 0.13
katG 2156086 p.Thr9Ile missense_variant 0.18
PPE35 2168237 c.2376G>A synonymous_variant 0.2
Rv1979c 2222550 p.Tyr205* stop_gained 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288681 c.561A>T stop_lost&splice_region_variant 0.17
pncA 2289331 c.-90C>T upstream_gene_variant 0.14
pncA 2290108 c.-867C>A upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726398 p.Ser69Asn missense_variant 0.12
folC 2746536 p.Asn355Tyr missense_variant 0.13
folC 2746554 p.Phe349Leu missense_variant 0.14
folC 2747385 p.Thr72Ala missense_variant 0.15
pepQ 2859450 c.969C>T synonymous_variant 0.2
pepQ 2860472 c.-54G>A upstream_gene_variant 0.12
pepQ 2860530 c.-112T>C upstream_gene_variant 0.11
ribD 2987053 p.Asn72Ser missense_variant 0.22
Rv2752c 3065107 p.Val362Ala missense_variant 0.18
Rv2752c 3066133 p.Ala20Val missense_variant 0.17
thyX 3067679 c.266delG frameshift_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087866 c.1047G>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474201 c.195G>A synonymous_variant 0.18
fprA 3474236 p.Arg77His missense_variant 0.17
fprA 3474251 p.Val82Ala missense_variant 0.13
fprA 3474263 p.Glu86Val missense_variant 0.17
fprA 3474523 p.Leu173Met missense_variant 0.13
Rv3236c 3611974 c.1143A>C synonymous_variant 0.92
Rv3236c 3612160 c.957A>G synonymous_variant 0.17
Rv3236c 3612177 c.940C>A synonymous_variant 0.18
Rv3236c 3612654 c.463C>T synonymous_variant 0.13
fbiA 3640610 p.Leu23Pro missense_variant 0.25
fbiB 3642355 p.Asp274Val missense_variant 0.12
fbiB 3642375 p.Ala281Thr missense_variant 0.15
fbiB 3642694 p.Ala387Glu missense_variant 0.18
fbiB 3642723 p.Trp397Arg missense_variant 0.22
alr 3840341 c.1080C>G synonymous_variant 0.25
alr 3840824 p.Tyr199* stop_gained 0.17
alr 3841110 p.Gly104Asp missense_variant 0.15
alr 3841591 c.-171T>C upstream_gene_variant 0.2
rpoA 3878373 c.135G>T synonymous_variant 0.18
rpoA 3878382 c.126G>A synonymous_variant 0.2
rpoA 3878388 c.120C>T synonymous_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 0.33
clpC1 4039663 p.Gly348Ser missense_variant 0.12
clpC1 4040798 c.-94G>T upstream_gene_variant 0.15
embC 4239890 p.Ile10Phe missense_variant 0.12
embC 4241084 p.Leu408Val missense_variant 0.14
embC 4241114 p.Ala418Thr missense_variant 0.14
embC 4241121 p.Ser420Ile missense_variant 0.15
embC 4242464 p.Trp868Arg missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.83
embA 4243673 c.441C>T synonymous_variant 0.25
embA 4245972 p.Ile914Phe missense_variant 0.67
embB 4246694 c.186delG frameshift_variant 0.14
embB 4247700 p.Met396Lys missense_variant 0.14
embB 4248990 p.Ile826Thr missense_variant 0.18
embB 4249280 p.Gly923* stop_gained 0.14
embB 4249316 p.Ala935Thr missense_variant 0.2
embB 4249399 c.2886G>A synonymous_variant 0.2
embB 4249446 p.Val978Ala missense_variant 0.15
embB 4249543 c.3030G>A synonymous_variant 0.14
embB 4249544 p.Lys1011Gln missense_variant 0.13
aftB 4267151 c.1686C>A synonymous_variant 0.25
aftB 4267173 p.Asp555Gly missense_variant 0.33
ethR 4326744 c.-805G>A upstream_gene_variant 0.17
ethA 4328295 c.-822G>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407558 c.645G>A synonymous_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 0.11