TB-Profiler result

Run: SRR18391770

Summary

Run ID: SRR18391770

Sample name:

Date: 03-04-2023 19:43:04

Number of reads: 519304

Percentage reads mapped: 79.88

Strain: La1.7.1

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
La1.7 M.bovis None None 1.0
La1.7.1 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
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 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 491742 c.960T>C synonymous_variant 1.0
mshA 575583 p.Leu79Gln missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766245 p.Gln959Pro missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778488 p.Lys140Glu missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305332 p.Glu801Gly missense_variant 0.1
embR 1417423 c.-76G>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474946 n.1289C>T non_coding_transcript_exon_variant 0.22
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.12
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.25
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.25
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.19
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.19
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.19
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.19
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.19
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917897 c.-43T>C upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918609 p.Gly224Cys missense_variant 0.12
ndh 2101694 p.Ala450Asp missense_variant 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 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.31
PPE35 2170056 p.Val186Ala missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288897 c.345A>T synonymous_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518428 p.Pro105Leu missense_variant 0.15
kasA 2518809 p.Lys232Arg missense_variant 0.15
eis 2714581 p.Ala251Val missense_variant 0.12
eis 2714700 c.633C>T synonymous_variant 0.12
eis 2715088 p.Leu82Arg missense_variant 0.13
eis 2715103 p.Leu77Pro missense_variant 0.14
folC 2746543 c.1056C>T synonymous_variant 0.2
folC 2747294 p.Gln102Arg missense_variant 0.11
folC 2747526 p.Ala25Ser missense_variant 0.13
Rv2752c 3066387 c.-197delC upstream_gene_variant 0.1
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
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474121 p.Leu39Met missense_variant 0.17
fprA 3474366 c.360G>C synonymous_variant 0.13
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475276 p.Gln424Lys missense_variant 0.14
fbiA 3640636 p.Ser32Pro missense_variant 1.0
fbiB 3642478 p.Asp315Ala missense_variant 1.0
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
embC 4240843 c.981C>T synonymous_variant 0.11
embC 4242299 p.Gly813Arg missense_variant 0.33
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
embA 4244719 p.Tyr496Ser missense_variant 0.22
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T 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 4269549 c.-713C>T upstream_gene_variant 0.14
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269850 c.-17G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408085 p.Glu40Lys missense_variant 0.12