TB-Profiler result

Run: SRR1791711
Summary

Run ID: SRR1791711

Sample name:

Date: 03-04-2023 18:25:05

Number of reads: 353713

Percentage reads mapped: 99.4

Strain: La1.3

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
La1.3 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
gyrB 6792 p.Asp518Gly missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7430 p.Glu43Asp missense_variant 0.14
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 9304 p.Gly668Asp missense_variant 0.92
fgd1 490747 c.-36C>T upstream_gene_variant 0.11
fgd1 490751 c.-32T>G upstream_gene_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575424 p.Arg26His missense_variant 0.13
ccsA 620542 p.Arg218Trp missense_variant 0.14
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoB 761438 c.1632G>A synonymous_variant 0.12
rpoB 762588 p.Thr928Ala missense_variant 0.11
rpoB 762987 p.Arg1061Trp missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764349 p.Met327Thr missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777902 c.579C>A synonymous_variant 0.15
mmpL5 778465 p.Thr6Ala missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781418 c.-142G>T upstream_gene_variant 0.15
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304724 c.1794A>G synonymous_variant 0.12
embR 1416617 p.Gly244Asp missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473795 n.138G>T non_coding_transcript_exon_variant 0.15
rrl 1474132 n.475G>A non_coding_transcript_exon_variant 0.12
rrl 1474621 n.964A>G non_coding_transcript_exon_variant 0.13
rrl 1475345 n.1688T>C non_coding_transcript_exon_variant 0.13
rrl 1476728 n.3071T>C non_coding_transcript_exon_variant 1.0
inhA 1674785 p.Arg195Gln missense_variant 1.0
inhA 1674867 p.Trp222* stop_gained 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
rpsA 1834968 p.Lys476Arg missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.22
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 2169870 p.Gly248Asp missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2222067 c.1098G>A synonymous_variant 0.14
Rv1979c 2222212 p.Ala318Val missense_variant 0.11
Rv1979c 2222306 p.Asp287Asn missense_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289565 c.-324G>T upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.25
kasA 2518991 p.Arg293Cys missense_variant 0.12
eis 2714797 p.Tyr179Phe missense_variant 0.11
eis 2715152 p.Met61Val missense_variant 1.0
ahpC 2726295 p.Phe35Leu missense_variant 0.13
ribD 2987607 p.Lys257Glu missense_variant 0.1
Rv2752c 3067106 c.-916dupC upstream_gene_variant 0.11
thyA 3074645 c.-174T>G upstream_gene_variant 0.38
thyA 3074648 c.-177T>G upstream_gene_variant 0.25
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
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474638 p.Glu211Val missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612427 c.690G>A synonymous_variant 0.25
Rv3236c 3612977 p.Gly47Asp missense_variant 0.25
Rv3236c 3613296 c.-180T>C upstream_gene_variant 0.33
fbiA 3641048 p.Phe169Ser missense_variant 0.12
rpoA 3877646 p.Asn288Asp missense_variant 0.11
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038712 p.Thr665Ala missense_variant 0.11
clpC1 4039155 p.Arg517Gln missense_variant 0.11
embC 4240048 c.186C>A synonymous_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241141 p.Ile427Val missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245867 p.Ser879Pro missense_variant 0.22
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246838 p.Ala109Thr missense_variant 0.15
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267035 p.Arg601His missense_variant 1.0
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
aftB 4269600 c.-764C>A upstream_gene_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4328023 c.-550G>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407886 p.Thr106Ile missense_variant 0.12
gid 4408057 p.Leu49Pro missense_variant 0.11
gid 4408261 c.-59G>A upstream_gene_variant 1.0
whiB7 3568430 c.-595_249del conservative_inframe_deletion 1.0