TB-Profiler result

Run: ERR2747602
Summary

Run ID: ERR2747602

Sample name:

Date: 31-03-2023 23:27:52

Number of reads: 209055

Percentage reads mapped: 56.24

Strain: lineage4.9;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 0.21
La1.8 M.bovis None None 1.0
La1.8.1 M.bovis None None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 0.81
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 7150 c.-152G>A upstream_gene_variant 0.5
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 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
mshA 576089 p.Arg248Cys missense_variant 0.33
mshA 576136 c.789T>C synonymous_variant 0.17
ccsA 620282 p.Arg131His missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1407155 c.186C>A synonymous_variant 0.22
embR 1416960 p.Arg130Trp missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673840 p.Arg134Gln missense_variant 0.29
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917976 c.37C>A synonymous_variant 0.29
ndh 2102193 p.Arg284Trp missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_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 0.5
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
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
ald 3087446 c.627C>T synonymous_variant 0.5
Rv3083 3448662 c.159T>A synonymous_variant 0.5
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449618 p.Thr372Ile missense_variant 0.5
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
fbiA 3640472 c.-71G>A upstream_gene_variant 0.13
fbiB 3642515 c.981C>A synonymous_variant 0.33
alr 3841220 c.201C>T synonymous_variant 0.2
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040582 c.123G>A synonymous_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241258 c.1396C>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242813 p.Asp984Val missense_variant 0.17
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embC 4242981 p.Met1040Thr missense_variant 1.0
embC 4243008 p.Leu1049Pro missense_variant 0.2
embA 4243340 c.108G>A synonymous_variant 0.2
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244914 p.Leu561Pro missense_variant 0.29
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 4249796 p.Arg1095Gly missense_variant 0.22
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 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326966 p.Asp170Tyr missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407869 p.Val112Ile missense_variant 0.29