TB-Profiler result

Run: SRR18391669
Summary

Run ID: SRR18391669

Sample name:

Date: 03-04-2023 19:39:19

Number of reads: 459340

Percentage reads mapped: 98.2

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 9010 p.Phe570Ser missense_variant 0.11
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 490828 p.Ala16Pro missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576090 p.Arg248Leu missense_variant 0.18
mshA 576119 p.Ala258Ser missense_variant 0.18
ccsA 620609 p.Phe240Ser missense_variant 0.18
ccsA 620720 p.Ala277Glu missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766339 p.Asp990Glu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775806 p.Met892Lys missense_variant 0.12
mmpL5 775912 p.Arg857Trp missense_variant 0.12
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
fbiC 1303615 p.Ala229Thr missense_variant 0.13
fbiC 1305284 p.Gln785Arg missense_variant 0.1
fbiC 1305412 p.Lys828Glu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471754 n.-92T>C upstream_gene_variant 0.12
rrl 1474562 n.905G>T non_coding_transcript_exon_variant 0.5
rrl 1474711 n.1054G>T non_coding_transcript_exon_variant 0.18
rrl 1474828 n.1171G>T non_coding_transcript_exon_variant 0.18
rrl 1475431 n.1774T>C non_coding_transcript_exon_variant 0.33
rrl 1476041 n.2384A>G non_coding_transcript_exon_variant 0.5
rrl 1476475 n.2818T>C non_coding_transcript_exon_variant 0.25
rrl 1476562 n.2905C>T non_coding_transcript_exon_variant 0.18
inhA 1674201 c.-1C>G upstream_gene_variant 0.11
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917984 c.45C>T synonymous_variant 0.15
tlyA 1918555 c.616C>A synonymous_variant 0.12
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155154 p.Val320Leu missense_variant 0.12
katG 2155417 p.Pro232Gln missense_variant 0.13
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 2169022 p.Gly531Arg missense_variant 0.15
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
eis 2715387 c.-55T>C upstream_gene_variant 0.13
Rv2752c 3066030 p.Glu54Asp missense_variant 0.12
thyX 3067340 p.Glu202Asp missense_variant 0.14
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 3339518 p.His134Arg missense_variant 0.11
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449097 c.594C>A synonymous_variant 0.15
Rv3083 3449123 p.Val207Ala missense_variant 0.15
Rv3083 3449248 p.Ala249Ser missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474118 p.Met38Val missense_variant 0.11
fprA 3474253 p.Val83Phe missense_variant 0.12
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568518 c.162C>A synonymous_variant 0.14
fbiB 3642478 p.Asp315Ala missense_variant 1.0
fbiB 3642875 c.1341G>A synonymous_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038390 p.Pro772Gln missense_variant 0.12
clpC1 4038403 c.2302T>C synonymous_variant 1.0
panD 4044272 p.Thr4Ser missense_variant 0.12
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
embA 4245507 p.Gly759Arg missense_variant 0.15
embB 4246061 c.-453C>A upstream_gene_variant 0.15
embB 4246259 c.-255G>T upstream_gene_variant 0.12
embA 4246459 p.Glu1076Val missense_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247002 c.489G>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247650 c.1137C>A synonymous_variant 0.13
embB 4249672 c.3159G>A synonymous_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268624 c.213C>A synonymous_variant 0.2
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 4326071 p.Ile468Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0