TB-Profiler result

Run: ERR4769421
Summary

Run ID: ERR4769421

Sample name:

Date: 01-04-2023 06:39:48

Number of reads: 3008453

Percentage reads mapped: 87.56

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 0.96
gyrB 6446 p.Ala403Ser missense_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 7821 c.520C>T synonymous_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 0.96
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9419 c.2118T>C synonymous_variant 0.13
gyrA 9420 p.Ile707Ala missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>G upstream_gene_variant 1.0
rpoC 763034 c.-336C>G upstream_gene_variant 0.19
rpoC 763040 c.-330C>G upstream_gene_variant 0.21
rpoC 763070 c.-300T>C upstream_gene_variant 0.18
rpoC 764431 c.1062G>C synonymous_variant 0.16
rpoC 764434 c.1065A>G synonymous_variant 0.16
rpoC 764452 c.1083T>C synonymous_variant 0.13
rpoC 764458 c.1089G>C synonymous_variant 0.14
rpoC 764461 c.1092A>G synonymous_variant 0.14
rpoC 764485 c.1116G>C synonymous_variant 0.14
rpoC 764491 c.1122G>T synonymous_variant 0.13
rpoC 764497 c.1128A>G synonymous_variant 0.13
rpoC 764500 c.1131C>G synonymous_variant 0.13
rpoC 764521 c.1152T>C synonymous_variant 0.16
rpoC 764527 c.1158C>T synonymous_variant 0.14
rpoC 764539 c.1170C>G synonymous_variant 0.12
rpoC 764650 c.1281G>T synonymous_variant 0.14
rpoC 764791 c.1422C>G synonymous_variant 0.15
rpoC 764815 c.1446A>G synonymous_variant 0.13
rpoC 764824 c.1455T>C synonymous_variant 0.13
rpoC 766804 c.3435A>G synonymous_variant 0.12
rpoC 766996 c.3627C>T synonymous_variant 0.14
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 0.99
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.15
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.17
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.18
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.21
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.17
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.2
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.15
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.16
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.15
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.15
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.17
rrl 1474282 n.625G>A non_coding_transcript_exon_variant 0.15
rrl 1474293 n.637_644delCCTCTCCG non_coding_transcript_exon_variant 0.17
rrl 1474303 n.646A>T non_coding_transcript_exon_variant 0.2
rrl 1474306 n.649A>T non_coding_transcript_exon_variant 0.2
rrl 1474308 n.653_654delTG non_coding_transcript_exon_variant 0.2
rrl 1474350 n.693G>C non_coding_transcript_exon_variant 0.17
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.18
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.16
rrl 1474374 n.717T>G non_coding_transcript_exon_variant 0.12
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.21
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.23
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.23
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.27
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.22
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.14
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.14
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.13
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.18
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.17
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.13
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.2
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.16
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.12
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.13
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.17
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.17
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.24
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.24
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.26
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.16
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.17
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.27
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.22
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.23
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.25
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.22
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.15
rpsA 1833841 c.300C>G synonymous_variant 0.12
rpsA 1833874 c.333T>C synonymous_variant 0.13
rpsA 1833892 c.351G>A synonymous_variant 0.13
rpsA 1834859 p.Ala440Thr missense_variant 0.99
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 0.98
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 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
Rv2752c 3065888 p.Val102Ile missense_variant 1.0
thyX 3067786 p.Thr54Ala missense_variant 0.97
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 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
rpoA 3877856 c.652T>C synonymous_variant 0.13
rpoA 3877866 c.642G>C synonymous_variant 0.13
rpoA 3877875 c.633T>C synonymous_variant 0.14
rpoA 3877971 p.Asp179Glu missense_variant 0.13
rpoA 3878160 c.348C>G synonymous_variant 0.13
rpoA 3878187 c.321C>G synonymous_variant 0.14
rpoA 3878193 c.315T>C synonymous_variant 0.16
rpoA 3878205 c.303T>C synonymous_variant 0.15
rpoA 3878217 c.291A>G synonymous_variant 0.17
rpoA 3878247 c.261G>C synonymous_variant 0.18
rpoA 3878253 c.255G>C synonymous_variant 0.15
rpoA 3878256 c.252G>C synonymous_variant 0.13
rpoA 3878264 p.Ser82Gly missense_variant 0.15
rpoA 3878630 c.-124delC upstream_gene_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 0.99
embB 4247173 c.660G>A synonymous_variant 0.99
embB 4247646 p.Glu378Ala missense_variant 0.99
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
gid 4407743 p.Arg154Trp missense_variant 1.0