TB-Profiler result

Run: ERR2747597
Summary

Run ID: ERR2747597

Sample name:

Date: 31-03-2023 23:27:49

Number of reads: 596186

Percentage reads mapped: 76.61

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
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrB 5810 p.Ala191Pro missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8048 c.747C>A synonymous_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
fgd1 491674 p.Gly298Cys missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620197 p.Gln103Lys missense_variant 0.12
rpoB 762709 p.Thr968Met missense_variant 0.4
rpoB 762832 c.3027delC frameshift_variant 0.25
rpoB 762879 p.Met1025Leu missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764015 c.646C>T synonymous_variant 0.17
rpoC 764246 p.Leu293Ile missense_variant 0.17
rpoC 764566 c.1197C>T synonymous_variant 0.15
rpoC 765633 p.Lys755Met missense_variant 0.15
rpoC 766278 p.Thr970Ile missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778451 c.-539C>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781696 p.Asn46Ile missense_variant 0.2
rplC 800900 p.Ala31Val missense_variant 0.29
rplC 801154 p.Gly116Cys missense_variant 0.2
rplC 801454 p.Glu216Gln missense_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303190 p.Ser87* stop_gained 0.17
fbiC 1305197 p.Ala756Glu missense_variant 0.29
fbiC 1305450 c.2520C>A synonymous_variant 0.17
embR 1416981 p.Val123Leu missense_variant 0.22
atpE 1460938 c.-107C>T upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471935 n.90T>C non_coding_transcript_exon_variant 1.0
rrl 1474369 n.712A>G non_coding_transcript_exon_variant 0.5
inhA 1673715 c.-487C>G upstream_gene_variant 1.0
inhA 1674144 c.-58G>A upstream_gene_variant 0.25
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918598 p.Trp220* stop_gained 0.18
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168145 p.Pro823Leu missense_variant 0.4
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169841 p.Gly258Ser missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222726 p.Val147Met missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288698 p.Leu182Met missense_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
ribD 2987582 c.744C>A synonymous_variant 0.15
Rv2752c 3064680 c.1512C>A synonymous_variant 0.12
thyX 3067935 p.Thr4Ile missense_variant 0.14
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086945 c.126C>A synonymous_variant 0.12
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 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3611985 p.Pro378Ser missense_variant 0.15
Rv3236c 3612536 p.Gly194Val missense_variant 0.18
Rv3236c 3613273 c.-157C>A upstream_gene_variant 0.15
fbiA 3641159 p.Ala206Val missense_variant 0.2
fbiB 3642369 p.Ala279Ser missense_variant 0.18
alr 3841162 p.Ala87Pro missense_variant 0.2
alr 3841171 p.Ala84Pro missense_variant 0.22
alr 3841334 c.87C>T synonymous_variant 0.29
rpoA 3877995 c.513G>A synonymous_variant 0.15
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3986945 c.102G>C synonymous_variant 0.29
ddn 3987023 c.180G>A synonymous_variant 0.4
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040157 p.Met183Thr missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242642 p.Arg927His missense_variant 1.0
embC 4242693 p.Arg944Leu missense_variant 0.22
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243751 c.519C>T synonymous_variant 0.29
embA 4243882 p.Ala217Asp missense_variant 0.18
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244602 p.Ala457Glu missense_variant 0.18
embA 4245150 p.Val640Ile missense_variant 0.22
embA 4246460 p.Glu1076Asp missense_variant 0.2
embA 4246491 p.Pro1087Thr missense_variant 0.2
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246621 c.110delG frameshift_variant 0.22
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247053 c.540C>T synonymous_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248734 p.Arg741Trp missense_variant 1.0
aftB 4267167 p.Gln557Pro missense_variant 1.0
aftB 4267341 p.Gly499Val missense_variant 0.18
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268310 c.526delG frameshift_variant 0.18
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 4269910 c.-77C>A upstream_gene_variant 0.14
ethA 4326024 p.Pro484Ser missense_variant 1.0
ethA 4326618 p.Tyr286His missense_variant 0.2
ethA 4327089 p.Leu129Ile missense_variant 0.12
ethR 4327734 c.188delT frameshift_variant 0.33
ethR 4327796 p.Ala83Val missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408331 c.-129C>T upstream_gene_variant 0.15