TB-Profiler result

Run: SRR1657056
Summary

Run ID: SRR1657056

Sample name:

Date: 03-04-2023 17:43:45

Number of reads: 681658

Percentage reads mapped: 54.87

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
pncA 2289150 p.Ile31Thr missense_variant 0.18 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
gyrB 5836 p.Phe199Leu missense_variant 0.22
gyrB 6252 p.Leu338Pro missense_variant 0.18
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 7973 c.672A>G synonymous_variant 0.11
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 9492 p.Tyr731His missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576788 c.1441T>C stop_lost&splice_region_variant 0.22
rpoB 760418 c.612G>A synonymous_variant 0.14
rpoB 760438 p.Asp211Val missense_variant 0.12
rpoB 760465 p.Ile220Asn missense_variant 0.14
rpoB 760480 p.Arg225Pro missense_variant 0.12
rpoB 762157 p.Val784Glu missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765890 p.Arg841Cys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776542 p.Ser647Gly missense_variant 0.13
mmpL5 777597 p.Arg295Gln missense_variant 0.18
mmpL5 778213 p.Ala90Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800808 c.-1A>G upstream_gene_variant 0.13
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304357 p.Ile476Asn missense_variant 0.12
Rv1258c 1407391 c.-51A>G upstream_gene_variant 0.22
embR 1416826 c.522T>C synonymous_variant 0.11
atpE 1461019 c.-26C>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473040 n.1195C>A non_coding_transcript_exon_variant 0.22
inhA 1673586 c.-616C>T upstream_gene_variant 0.33
fabG1 1673794 p.Val119Met missense_variant 0.2
rpsA 1833684 p.Arg48Leu missense_variant 0.11
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917827 c.-113C>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918577 p.Arg213Gln missense_variant 0.18
ndh 2102226 p.Cys273Arg missense_variant 0.2
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 2155503 c.609C>T synonymous_variant 1.0
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 2168086 p.Glu843Lys missense_variant 0.18
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170465 p.Ala50Pro missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222523 c.642C>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.14
kasA 2518217 p.Gly35Cys missense_variant 0.11
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2746198 c.1401C>T synonymous_variant 0.18
pepQ 2859740 p.Ala227Thr missense_variant 0.25
thyX 3067643 c.303C>T synonymous_variant 0.13
thyX 3068114 c.-169G>A upstream_gene_variant 0.13
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 3474705 c.699T>C synonymous_variant 0.1
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612737 p.Ile127Thr missense_variant 0.14
Rv3236c 3613244 c.-128G>A upstream_gene_variant 0.14
Rv3236c 3613247 c.-131C>T upstream_gene_variant 1.0
fbiA 3640429 c.-114C>T upstream_gene_variant 1.0
fbiB 3642393 p.Pro287Ala missense_variant 0.11
alr 3841493 c.-73A>G upstream_gene_variant 0.12
rpoA 3878630 c.-124delC upstream_gene_variant 0.91
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038695 c.2010C>A synonymous_variant 0.14
embC 4240374 p.Leu171Arg missense_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241061 p.Pro400Leu missense_variant 0.14
embC 4241871 p.Val670Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243569 p.Thr113Ala missense_variant 0.1
embA 4243889 c.657G>A synonymous_variant 0.33
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245165 p.Pro645Thr missense_variant 0.22
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248202 c.1689T>A synonymous_variant 0.15
aftB 4267546 p.Asp431Asn missense_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4267938 p.Arg300Gln missense_variant 0.2
aftB 4268281 p.Arg186Trp missense_variant 0.12
aftB 4268844 c.-8A>G upstream_gene_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269538 p.Glu99Gly missense_variant 0.29
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 0.14
ethA 4326842 p.Tyr211Cys missense_variant 0.13
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
gid 4407932 p.Leu91Ile missense_variant 0.13