TB-Profiler result

Run: ERR4772204
Summary

Run ID: ERR4772204

Sample name:

Date: 01-04-2023 06:44:51

Number of reads: 1153501

Percentage reads mapped: 98.69

Strain: La1.2

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
La1.2 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 5475 p.Asp79Val missense_variant 0.12
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 6488 p.Arg417Ser missense_variant 0.14
gyrA 6535 c.-767C>A upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7821 c.520C>T synonymous_variant 1.0
gyrA 7990 p.Thr230Ser missense_variant 0.12
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 490602 c.-181C>T upstream_gene_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575921 p.Asp192Asn missense_variant 0.18
mshA 576376 c.1029G>C synonymous_variant 0.11
rpoB 761019 p.Ala405Ser missense_variant 0.12
rpoB 761050 p.Arg415Gln missense_variant 0.14
rpoB 761386 p.Ala527Asp missense_variant 0.14
rpoB 762360 p.Glu852* stop_gained 0.14
rpoB 762371 p.Leu855Phe missense_variant 0.13
rpoB 762775 p.Arg990Leu missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763221 p.Ile1139Phe missense_variant 0.17
rpoC 764840 p.Ile491Val missense_variant 0.11
rpoC 765445 c.2076G>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777219 p.Leu421Pro missense_variant 0.11
mmpL5 777935 c.546C>A synonymous_variant 0.18
mmpR5 778076 c.-914G>A upstream_gene_variant 0.13
mmpL5 779256 c.-776C>A upstream_gene_variant 0.18
mmpL5 779424 c.-944A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781774 p.His72Leu missense_variant 0.22
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304112 c.1182G>C synonymous_variant 0.11
fbiC 1304682 c.1752C>A synonymous_variant 0.12
Rv1258c 1406110 p.Ile411Phe missense_variant 0.12
Rv1258c 1406539 p.Ala268Ser missense_variant 0.13
Rv1258c 1406971 p.Arg124Cys missense_variant 0.2
Rv1258c 1407253 p.Phe30Leu missense_variant 0.25
embR 1416861 p.Ala163Ser missense_variant 0.2
embR 1417513 c.-166A>G upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472220 n.375G>T non_coding_transcript_exon_variant 0.17
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.4
rrs 1472767 n.922G>T non_coding_transcript_exon_variant 0.17
rrs 1472957 n.1112C>A non_coding_transcript_exon_variant 0.12
rrs 1473314 n.1469A>T non_coding_transcript_exon_variant 0.14
rrl 1473610 n.-48C>T upstream_gene_variant 0.14
rrl 1475535 n.1878G>T non_coding_transcript_exon_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
fabG1 1673823 p.Gln128His missense_variant 0.15
fabG1 1674013 p.Arg192Ser missense_variant 0.22
inhA 1674248 p.Ile16Asn missense_variant 0.12
inhA 1674334 c.133C>A synonymous_variant 0.14
inhA 1674786 c.585G>T synonymous_variant 0.14
rpsA 1833502 c.-40T>C upstream_gene_variant 0.25
rpsA 1834747 p.Glu402Asp missense_variant 0.17
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 p.Gly313Arg missense_variant 1.0
ndh 2102278 c.765C>T synonymous_variant 0.15
ndh 2102939 p.Arg35Leu missense_variant 0.13
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155210 p.Lys301Arg missense_variant 0.25
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155560 c.552C>A synonymous_variant 0.29
katG 2155675 p.Arg146Gln missense_variant 0.17
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167713 p.Val967Ala missense_variant 0.13
PPE35 2167884 p.Gly910Asp missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
Rv1979c 2221989 c.1176T>C synonymous_variant 0.12
Rv1979c 2222152 p.Thr338Lys missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289137 c.105G>T synonymous_variant 0.18
pncA 2290005 c.-764G>C upstream_gene_variant 0.15
pncA 2290028 c.-787C>A upstream_gene_variant 0.14
kasA 2518126 c.12T>C synonymous_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518246 p.His44Gln missense_variant 0.14
kasA 2518267 c.153C>A synonymous_variant 0.18
kasA 2518735 c.621C>A synonymous_variant 0.13
eis 2715547 c.-215A>C upstream_gene_variant 0.12
ahpC 2726256 p.Asp22His missense_variant 0.25
ahpC 2726374 p.Cys61Phe missense_variant 0.18
folC 2746434 p.Gly389Ser missense_variant 0.17
folC 2746965 c.633dupG frameshift_variant 0.18
pepQ 2859360 c.1059A>G synonymous_variant 0.11
pepQ 2860094 p.Ala109Thr missense_variant 0.14
ribD 2987030 c.192G>T synonymous_variant 0.15
ribD 2987614 c.776G>T stop_lost&splice_region_variant 0.12
Rv2752c 3065888 p.Val102Ile missense_variant 1.0
Rv2752c 3066196 c.-5C>T upstream_gene_variant 0.13
thyX 3067786 p.Thr54Ala missense_variant 1.0
thyX 3067789 p.Lys53* stop_gained 0.22
thyX 3068052 c.-107C>A upstream_gene_variant 0.13
thyA 3074033 p.His147Asn missense_variant 0.33
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087020 p.Asp67Glu missense_variant 0.12
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087231 p.Gly138Ser missense_variant 0.2
fbiD 3339154 p.Ile13Leu missense_variant 1.0
fbiD 3339746 p.Ala210Val missense_variant 0.12
Rv3083 3448526 p.Leu8Pro missense_variant 0.15
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473891 c.-116A>C upstream_gene_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
fprA 3475285 p.Asp427Asn missense_variant 0.13
whiB7 3568680 c.-1C>G upstream_gene_variant 0.15
Rv3236c 3612889 p.Glu76Asp missense_variant 0.15
fbiA 3641105 p.Val188Asp missense_variant 0.18
fbiA 3641218 p.Val226Phe missense_variant 0.15
alr 3840444 p.Leu326Pro missense_variant 0.13
alr 3840871 p.Ala184Ser missense_variant 0.12
alr 3841580 c.-160C>A upstream_gene_variant 0.17
rpoA 3878677 c.-170C>A upstream_gene_variant 0.33
rpoA 3878680 c.-173C>T upstream_gene_variant 0.33
ddn 3986681 c.-163C>A upstream_gene_variant 0.12
ddn 3986760 c.-84G>T upstream_gene_variant 0.17
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039506 p.Ile400Asn missense_variant 0.18
clpC1 4040192 c.513C>A synonymous_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241298 p.Ala479Glu missense_variant 0.33
embC 4241464 c.1602C>A synonymous_variant 0.15
embC 4241722 c.1860C>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243317 p.Gly29Ser missense_variant 0.13
embA 4243632 p.Gly134* stop_gained 0.18
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244741 p.Tyr503* stop_gained 0.13
embA 4245313 p.Ala694Val missense_variant 0.15
embA 4245628 p.Pro799His missense_variant 0.15
embB 4246103 c.-411C>A upstream_gene_variant 0.12
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4267984 p.Arg285Cys missense_variant 0.33
ubiA 4269297 c.536delT frameshift_variant 0.22
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 4270004 c.-171G>T upstream_gene_variant 0.14
ethA 4326435 p.Gln347Lys missense_variant 0.13
ethR 4327997 p.Ala150Asp missense_variant 0.17
whiB6 4338501 c.21A>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407743 p.Arg154Trp missense_variant 1.0
gid 4407838 p.Ser122Tyr missense_variant 0.13