TB-Profiler result

Run: SRR1657063
Summary

Run ID: SRR1657063

Sample name:

Date: 03-04-2023 17:43:54

Number of reads: 813482

Percentage reads mapped: 98.99

Strain: La1.8.1

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
La1.8 M.bovis None None 1.0
La1.8.1 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
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
gyrA 9710 p.Leu803Phe missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764417 p.Arg350Cys missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776686 p.Ser599Ala missense_variant 0.14
mmpL5 776694 p.Val596Arg missense_variant 0.14
mmpL5 776702 c.1779C>T synonymous_variant 0.14
mmpL5 776726 c.1755C>T synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781432 c.-128T>C upstream_gene_variant 0.17
rplC 801038 p.Pro77Gln missense_variant 0.17
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406673 p.Arg223Gln missense_variant 0.25
Rv1258c 1406859 p.Gly161Asp missense_variant 0.33
Rv1258c 1407468 c.-128C>T upstream_gene_variant 0.25
embR 1416222 p.Phe376Leu missense_variant 0.33
embR 1416232 p.Cys372Gly missense_variant 0.33
embR 1416259 c.1089G>C synonymous_variant 0.11
atpE 1460930 c.-115C>T upstream_gene_variant 0.14
atpE 1461157 p.Gly38Asp missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474077 n.420G>A non_coding_transcript_exon_variant 0.17
rrl 1475982 n.2325G>T non_coding_transcript_exon_variant 0.33
fabG1 1673411 c.-28delG upstream_gene_variant 1.0
inhA 1673561 c.-641A>G upstream_gene_variant 0.11
rpsA 1833836 p.Arg99Trp missense_variant 0.25
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918259 p.His107Pro missense_variant 0.25
ndh 2102738 p.Glu102Gly missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155442 p.Gln224Lys missense_variant 0.17
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155600 p.Cys171Tyr missense_variant 0.14
katG 2155894 p.Val73Ala missense_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
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 2168818 p.Gly599Ser missense_variant 0.2
PPE35 2170400 c.213G>C synonymous_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222913 c.252C>T synonymous_variant 0.17
Rv1979c 2223060 c.105T>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714447 c.886T>C synonymous_variant 0.33
eis 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726225 c.33C>A synonymous_variant 0.11
folC 2747103 p.Ala166Thr missense_variant 0.25
folC 2747682 c.-84C>A upstream_gene_variant 0.14
pepQ 2859698 p.Lys241Glu missense_variant 0.14
ribD 2986641 c.-198G>A upstream_gene_variant 0.11
thyA 3074495 c.-24C>G upstream_gene_variant 0.17
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 3339608 p.Pro164Leu missense_variant 0.17
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 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613247 c.-131C>T upstream_gene_variant 1.0
fbiA 3640429 c.-114C>T upstream_gene_variant 1.0
rpoA 3878244 p.Glu88Asp missense_variant 0.25
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4239839 c.-24C>A upstream_gene_variant 0.17
embC 4239850 c.-13A>T upstream_gene_variant 0.14
embC 4240405 c.543T>C synonymous_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241218 c.1356G>T synonymous_variant 0.17
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
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246584 p.Arg24Leu missense_variant 0.17
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248597 p.Glu695Val missense_variant 0.14
embB 4248715 c.2202C>G synonymous_variant 0.13
embB 4249238 p.Ala909Ser missense_variant 0.25
aftB 4267230 p.Trp536* stop_gained 0.22
aftB 4267241 c.1596G>A synonymous_variant 0.15
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268844 c.-8A>G upstream_gene_variant 1.0
ubiA 4269124 p.Ala237Asp missense_variant 0.17
ubiA 4269178 p.Arg219Pro missense_variant 0.15
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
ubiA 4269885 c.-52C>T upstream_gene_variant 0.12
ethA 4327409 p.His22Leu missense_variant 0.14
ethA 4328196 c.-723G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0