TB-Profiler result

Run: SRR13199726
Summary

Run ID: SRR13199726

Sample name:

Date: 03-04-2023 08:22:56

Number of reads: 934595

Percentage reads mapped: 94.15

Strain: La1.2

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
La1.2 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 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
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 0.98
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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764742 p.Lys458Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.13
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.12
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.12
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.12
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.12
rrs 1473096 n.1251C>T non_coding_transcript_exon_variant 0.14
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473113 n.1268G>A non_coding_transcript_exon_variant 0.12
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.19
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.19
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.2
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.2
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.2
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.2
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.17
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.16
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.16
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.14
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.12
rrl 1474384 n.727C>T non_coding_transcript_exon_variant 0.11
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.13
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.13
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.12
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.12
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.12
rrl 1474964 n.1307T>A non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
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 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
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 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
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
fbiD 3339154 p.Ile13Leu missense_variant 1.0
Rv3083 3448745 p.Ile81Ser missense_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
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile 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 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 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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0