TB-Profiler result

Run: SRR13986560
Summary

Run ID: SRR13986560

Sample name:

Date: 03-04-2023 09:43:49

Number of reads: 730002

Percentage reads mapped: 38.67

Strain: La1.7

Drug-resistance: Other

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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
La1 M.bovis None None 1.0
La1.7 M.bovis None None 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
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.2
fgd1 491469 c.687C>A synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.29
ccsA 620064 c.174C>T synonymous_variant 0.29
ccsA 620797 p.Met303Leu missense_variant 0.18
rpoB 759620 c.-187A>C upstream_gene_variant 0.3
rpoB 760463 c.657C>A synonymous_variant 0.14
rpoB 761364 p.Asp520Asn missense_variant 0.13
rpoB 762726 p.Ala974Ser missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775624 p.Pro953Thr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775883 p.Ile866Leu missense_variant 0.18
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776566 p.Pro639Thr missense_variant 0.12
mmpL5 777648 p.Ala278Val missense_variant 0.12
mmpL5 777811 p.Arg224Trp missense_variant 0.22
mmpL5 778056 p.Ser142Thr missense_variant 0.12
mmpR5 778064 c.-926G>C upstream_gene_variant 0.12
mmpR5 778073 c.-917G>C upstream_gene_variant 0.12
mmpR5 778082 c.-908T>C upstream_gene_variant 0.14
mmpR5 778088 c.-902C>G upstream_gene_variant 0.14
mmpR5 778094 c.-896A>G upstream_gene_variant 0.12
mmpL5 779238 c.-758G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304266 p.Arg446Trp missense_variant 0.18
fbiC 1304432 p.Ser501Leu missense_variant 0.22
fbiC 1305490 p.Leu854Ile missense_variant 0.12
Rv1258c 1406752 p.Gly197Ser missense_variant 0.15
Rv1258c 1407046 p.Asp99Tyr missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476109 n.2455delG non_coding_transcript_exon_variant 0.11
rrl 1476131 n.2474C>G non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
inhA 1674807 c.606C>T synonymous_variant 0.25
rpsA 1834639 c.1098T>C synonymous_variant 0.11
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.23
PPE35 2169281 c.1332T>G synonymous_variant 0.23
PPE35 2169287 c.1326T>C synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289217 p.Val9Met missense_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518450 c.336C>A synonymous_variant 0.15
kasA 2518694 p.Val194Ile missense_variant 0.2
kasA 2518879 c.765A>G synonymous_variant 0.17
kasA 2518882 c.768C>A synonymous_variant 0.17
eis 2714299 p.Ala345Val missense_variant 1.0
eis 2714363 p.Ser324Pro missense_variant 1.0
eis 2714880 c.453C>A synonymous_variant 0.12
eis 2714957 p.Tyr126Asp missense_variant 0.12
folC 2747535 p.Asp22Tyr missense_variant 0.15
folC 2747762 c.-164G>A upstream_gene_variant 0.15
pepQ 2860162 p.Arg86Gln missense_variant 0.12
Rv2752c 3067158 c.-967G>A upstream_gene_variant 0.18
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
fbiD 3339264 c.147C>T synonymous_variant 0.2
Rv3083 3448641 c.138C>T synonymous_variant 0.15
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449005 p.His168Asn missense_variant 0.18
Rv3083 3449690 p.Thr396Asn missense_variant 0.12
fprA 3473965 c.-42A>G upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474299 p.Asp98Gly missense_variant 0.15
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612405 p.Ala238Pro missense_variant 0.11
Rv3236c 3612860 p.Leu86Arg missense_variant 0.11
fbiB 3641343 c.-192C>G upstream_gene_variant 0.25
fbiA 3641467 p.Leu309Met missense_variant 0.12
fbiB 3641878 p.Arg115Gln missense_variant 0.14
fbiB 3642085 p.Gly184Asp missense_variant 0.17
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038430 p.Leu759Val missense_variant 0.14
clpC1 4039373 p.Phe444Leu missense_variant 0.15
clpC1 4040061 p.Ile215Thr missense_variant 0.11
clpC1 4040681 c.24T>C synonymous_variant 1.0
panD 4044225 p.Asp19Glu missense_variant 0.12
embC 4240335 p.Thr158Ile missense_variant 0.12
embC 4240413 p.Leu184Gln missense_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242202 c.2340C>A synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242677 p.Thr939Ser missense_variant 0.22
embC 4242719 p.Ala953Thr missense_variant 0.18
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244641 p.Val470Gly missense_variant 0.25
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247312 p.Arg267Trp missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249066 c.2553C>T synonymous_variant 0.12
embB 4249766 p.Arg1085Cys missense_variant 0.33
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269582 p.His84Gln missense_variant 0.13
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326214 p.Glu420Asp missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0