TB-Profiler result

Run: SRR13986568
Summary

Run ID: SRR13986568

Sample name:

Date: 03-04-2023 09:44:06

Number of reads: 628840

Percentage reads mapped: 98.13

Strain: La1.2

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
La1.2 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 7692 p.Glu131Lys missense_variant 0.15
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491306 c.531_566delCGGCCCGGCGGTGGCCAAGTACGCCGGCCGCGCCGG disruptive_inframe_deletion 0.33
fgd1 491432 p.Ala217Asp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575666 p.Val107Leu missense_variant 0.12
mshA 575739 p.Ala131Val missense_variant 0.12
mshA 576113 p.Arg256Trp missense_variant 0.4
mshA 576652 p.Asp435Glu missense_variant 0.29
ccsA 620721 c.831G>A synonymous_variant 0.12
rpoB 761851 p.Pro682Leu missense_variant 0.12
rpoB 762757 p.Ser984* stop_gained 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766147 c.2778C>A synonymous_variant 0.12
rpoC 766973 p.Ala1202Ser missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777545 c.936C>T synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1407019 p.Val108Leu missense_variant 0.13
Rv1258c 1407535 c.-195G>T upstream_gene_variant 0.22
embR 1416232 p.Cys372Gly missense_variant 0.14
embR 1416891 p.Leu153Met missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472480 n.635G>A non_coding_transcript_exon_variant 0.2
rrs 1472878 n.1033G>A non_coding_transcript_exon_variant 0.12
rrl 1473870 n.213G>T non_coding_transcript_exon_variant 0.13
rrl 1474045 n.388C>T non_coding_transcript_exon_variant 0.22
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1475566 n.1909G>T non_coding_transcript_exon_variant 0.15
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 p.Gly313Arg missense_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
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169272 c.1341C>G synonymous_variant 0.11
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 2169902 p.Leu237Phe missense_variant 0.28
PPE35 2170247 p.Ile122Val missense_variant 0.12
PPE35 2170271 c.342T>C synonymous_variant 0.14
PPE35 2170280 c.333C>G synonymous_variant 0.13
PPE35 2170298 c.315A>G synonymous_variant 0.13
PPE35 2170308 p.Leu102Ala missense_variant 0.13
PPE35 2170313 c.300G>C synonymous_variant 0.13
PPE35 2170392 p.Gly74Ala missense_variant 0.21
PPE35 2170400 c.213G>C synonymous_variant 0.19
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288688 p.Ser185Asn missense_variant 0.13
pncA 2289237 p.Arg2Leu missense_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.21
kasA 2518505 p.Ala131Ser missense_variant 0.13
kasA 2518564 c.450C>A synonymous_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.14
kasA 2519143 c.1029G>C synonymous_variant 0.14
eis 2714944 p.Gly130Asp missense_variant 0.17
eis 2715154 p.Gly60Glu missense_variant 0.14
folC 2747671 c.-73C>T upstream_gene_variant 0.15
pepQ 2859627 p.Leu264Phe missense_variant 0.15
ribD 2987545 p.Thr236Asn missense_variant 0.15
thyX 3067569 p.Ala126Val missense_variant 0.15
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 3339154 p.Ile13Leu missense_variant 1.0
fbiD 3339510 c.393C>T synonymous_variant 0.22
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449118 c.615G>A synonymous_variant 0.67
Rv3083 3449318 p.Glu272Ala missense_variant 1.0
Rv3083 3449985 c.1482G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475317 p.His437Gln missense_variant 0.12
Rv3236c 3612352 c.765C>G synonymous_variant 0.17
Rv3236c 3612406 c.711C>T synonymous_variant 0.18
Rv3236c 3612409 c.708G>T synonymous_variant 0.17
fbiB 3641490 c.-45G>C upstream_gene_variant 0.11
fbiB 3642524 c.990G>T synonymous_variant 0.15
rpoA 3877677 c.831G>T synonymous_variant 0.13
rpoA 3877792 p.Ala239Val missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039498 p.Ile403Val missense_variant 0.12
clpC1 4039508 c.1197G>C synonymous_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.13
embC 4239667 c.-196C>A upstream_gene_variant 0.13
embC 4239774 c.-89C>T upstream_gene_variant 0.15
embC 4239783 c.-80C>A upstream_gene_variant 0.15
embC 4240201 c.339G>T synonymous_variant 0.12
embC 4240286 p.Ala142Ser missense_variant 0.15
embC 4240491 p.Pro210Arg missense_variant 0.5
embC 4240584 p.Thr241Asn missense_variant 0.25
embC 4240648 c.786C>T synonymous_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240905 p.Thr348Asn missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242773 p.Leu971Met missense_variant 0.18
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243378 p.Ser49Asn missense_variant 0.2
embA 4243451 c.219G>T synonymous_variant 0.18
embA 4243649 c.417G>T synonymous_variant 0.22
embA 4244095 p.Gly288Val missense_variant 0.18
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244810 c.1578C>T synonymous_variant 0.2
embA 4244989 p.Ala586Glu missense_variant 0.13
embA 4245450 c.2218C>T synonymous_variant 0.15
embB 4245602 c.-912C>A upstream_gene_variant 0.17
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247997 p.Ala495Val missense_variant 0.12
embB 4248062 p.Ala517Thr missense_variant 1.0
embB 4249152 p.Ala880Val missense_variant 0.25
embB 4249731 p.Ala1073Val missense_variant 0.15
aftB 4267831 p.Gly336Ser missense_variant 0.4
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269141 c.-305G>A upstream_gene_variant 0.22
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326229 c.1245C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407724 p.Leu160His missense_variant 0.15
gid 4407801 c.402G>A synonymous_variant 0.15