TB-Profiler result

Run: ERR4772207
Summary

Run ID: ERR4772207

Sample name:

Date: 01-04-2023 06:44:59

Number of reads: 1221929

Percentage reads mapped: 85.29

Strain: La1.3

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
La1.3 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
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 7072 p.Lys611Asn missense_variant 0.13
gyrA 7334 c.33G>A synonymous_variant 0.15
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
rpoB 760393 p.Val196Asp missense_variant 0.17
rpoB 760960 p.Val385Asp missense_variant 0.13
rpoB 762722 p.Asp972Glu missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775870 p.Ile871Val missense_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776128 p.Cys785Arg missense_variant 0.1
mmpL5 777795 p.Ser229* stop_gained 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800613 c.-196C>G upstream_gene_variant 0.12
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
embR 1416234 p.Cys372Ser missense_variant 0.13
embR 1417018 c.330C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472017 n.174dupG non_coding_transcript_exon_variant 0.17
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.12
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.12
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.11
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.11
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.12
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.11
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472953 n.1109_1112delTCTC non_coding_transcript_exon_variant 0.11
rrs 1472959 n.1114_1115insTTTA non_coding_transcript_exon_variant 0.12
rrs 1472971 n.1126G>T non_coding_transcript_exon_variant 0.12
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.12
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.13
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.13
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.13
rrs 1472991 n.1146G>A non_coding_transcript_exon_variant 0.13
rrs 1472992 n.1147A>T non_coding_transcript_exon_variant 0.14
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.13
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.13
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.13
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.22
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.17
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.17
rrs 1473136 n.1291A>G non_coding_transcript_exon_variant 0.12
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.11
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.18
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.47
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.47
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.4
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.38
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.38
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.31
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.27
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.2
rrl 1475154 n.1497C>A non_coding_transcript_exon_variant 0.22
rrl 1475167 n.1510T>A non_coding_transcript_exon_variant 0.25
rrl 1475175 n.1518G>A non_coding_transcript_exon_variant 0.33
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.13
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.14
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.13
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.14
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.14
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.25
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.27
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.17
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.29
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.4
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.4
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.4
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.36
rrl 1476391 n.2734C>T non_coding_transcript_exon_variant 0.17
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.28
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.11
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.19
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.31
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.45
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.39
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.12
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.13
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.24
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.15
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.11
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.12
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.17
rrl 1476728 n.3071T>C non_coding_transcript_exon_variant 1.0
fabG1 1674103 p.Ser222Gly missense_variant 0.1
inhA 1674504 c.303C>G synonymous_variant 0.12
rpsA 1834517 c.976C>T synonymous_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154065 p.Gly683Ser missense_variant 0.15
katG 2154418 p.Val565Glu missense_variant 0.13
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
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168362 p.Ile751Val missense_variant 0.12
PPE35 2168814 c.1798dupA frameshift_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
Rv2752c 3065159 p.Glu345* stop_gained 0.15
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 3087190 p.Asp124Gly missense_variant 0.14
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 3474448 c.445delC frameshift_variant 0.1
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840455 c.966G>T synonymous_variant 0.17
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240599 p.Val246Glu missense_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241384 p.Pro508Thr missense_variant 1.0
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 4246525 c.13delG frameshift_variant 0.18
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246582 c.69T>G synonymous_variant 0.29
embB 4246635 p.Ser41Leu missense_variant 0.17
embB 4246764 p.Pro84Gln missense_variant 0.12
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249640 c.3127T>C synonymous_variant 1.0
aftB 4267782 c.1054delG frameshift_variant 0.11
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 4326520 c.954A>G synonymous_variant 0.17
ethR 4326772 c.-777G>A upstream_gene_variant 0.11
ethA 4326821 p.Arg218Gln missense_variant 0.13
ethA 4326939 p.Val179Ile missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0