TB-Profiler result

Run: SRR18391723
Summary

Run ID: SRR18391723

Sample name:

Date: 03-04-2023 19:41:14

Number of reads: 200331

Percentage reads mapped: 65.06

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
gyrB 6585 p.Asp449Gly missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7761 p.Pro154Thr missense_variant 0.14
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8951 p.Lys550Asn missense_variant 0.15
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 575390 p.Gln15Lys missense_variant 0.2
mshA 575410 c.63C>G synonymous_variant 0.22
mshA 575910 p.Leu188Gln missense_variant 0.67
mshA 576239 p.Ala298Thr missense_variant 0.25
ccsA 619999 p.Ala37Ser missense_variant 0.67
ccsA 620128 p.Gly80Trp missense_variant 0.29
rpoB 761381 c.1575G>A synonymous_variant 0.22
rpoB 762159 p.Arg785Cys missense_variant 0.22
rpoB 762444 p.Ala880Thr missense_variant 0.22
rpoC 762590 c.-780C>A upstream_gene_variant 0.25
rpoC 762776 c.-594C>A upstream_gene_variant 0.4
rpoB 762861 p.Val1019Ile missense_variant 0.33
rpoC 762887 c.-483G>A upstream_gene_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764757 p.Leu463Pro missense_variant 0.12
rpoC 766129 c.2760C>A synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775811 p.Phe890Leu missense_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776378 p.Phe701Leu missense_variant 0.2
mmpL5 776745 p.Arg579Leu missense_variant 0.2
mmpL5 777529 p.Ala318Thr missense_variant 0.22
mmpL5 778366 p.Trp39Gly missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801079 p.Ala91Thr missense_variant 0.15
rplC 801415 p.Gly203Arg missense_variant 0.4
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305149 p.Val740Asp missense_variant 0.18
Rv1258c 1406474 c.867G>A synonymous_variant 0.2
embR 1416201 p.Gly383Trp missense_variant 0.15
embR 1416468 p.Asp294Tyr missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472055 n.210C>A non_coding_transcript_exon_variant 0.14
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.12
rrs 1472117 n.272A>G non_coding_transcript_exon_variant 0.12
rrs 1472856 n.1011T>A non_coding_transcript_exon_variant 0.12
rrs 1472923 n.1078G>A non_coding_transcript_exon_variant 0.17
rrs 1472934 n.1089C>T non_coding_transcript_exon_variant 0.15
rrl 1474566 n.909G>T non_coding_transcript_exon_variant 0.22
rrl 1475208 n.1551C>T non_coding_transcript_exon_variant 0.14
rrl 1475573 n.1916G>T non_coding_transcript_exon_variant 0.17
rrl 1475631 n.1974G>T non_coding_transcript_exon_variant 0.11
fabG1 1673552 c.114_115delCG frameshift_variant 0.18
inhA 1674503 p.Thr101Ile missense_variant 0.29
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918122 c.183C>T synonymous_variant 0.25
ndh 2101992 p.Leu351Met missense_variant 0.12
ndh 2102754 p.Gln97Lys missense_variant 0.29
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155104 c.1008G>A synonymous_variant 0.18
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167878 p.Ser912Asn missense_variant 0.5
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 2169249 p.Ile455Thr missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222973 c.192C>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289272 c.-31C>T upstream_gene_variant 0.2
kasA 2518024 c.-91C>A upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518716 p.Pro201His missense_variant 0.29
eis 2714608 p.Arg242Met missense_variant 0.22
eis 2714863 p.Gly157Val missense_variant 0.5
eis 2715218 p.Leu39Met missense_variant 0.18
ahpC 2726023 c.-170T>C upstream_gene_variant 0.33
folC 2746373 p.Pro409Gln missense_variant 0.22
ribD 2987495 c.657C>T synonymous_variant 0.25
thyX 3067861 p.Ala29Ser missense_variant 0.18
thyA 3074225 p.Trp83Arg missense_variant 0.12
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 3087776 c.957G>A synonymous_variant 0.14
fbiD 3338925 c.-193G>A upstream_gene_variant 0.29
fbiD 3339740 p.Ala208Val missense_variant 0.17
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448926 c.423C>A synonymous_variant 0.15
Rv3083 3449163 c.660G>A synonymous_variant 0.2
Rv3083 3449673 c.1170C>T synonymous_variant 0.2
Rv3083 3449882 p.Trp460Leu missense_variant 0.25
fprA 3473998 c.-9G>A upstream_gene_variant 0.67
fprA 3474350 p.Pro115His missense_variant 0.4
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475020 c.1014C>T synonymous_variant 0.4
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568435 p.Pro82Gln missense_variant 0.25
whiB7 3568442 p.Lys80Glu missense_variant 0.22
fbiA 3640636 p.Ser32Pro missense_variant 1.0
fbiB 3642135 p.Ala201Pro missense_variant 0.18
fbiB 3642170 c.636G>A synonymous_variant 0.18
fbiB 3642478 p.Asp315Ala missense_variant 1.0
alr 3840849 p.Arg191Leu missense_variant 0.22
alr 3841178 c.243C>A synonymous_variant 0.18
alr 3841492 c.-72C>T upstream_gene_variant 0.15
rpoA 3877496 p.Glu338Gln missense_variant 0.25
rpoA 3877754 p.Asp252Asn missense_variant 0.2
rpoA 3877899 c.609C>T synonymous_variant 0.2
rpoA 3878536 c.-29G>T upstream_gene_variant 0.5
ddn 3987251 p.Tyr136* stop_gained 0.29
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038947 c.1758C>T synonymous_variant 0.4
clpC1 4039112 c.1593C>T synonymous_variant 0.12
embC 4240201 c.339G>A synonymous_variant 0.25
embC 4240458 p.Gly199Val missense_variant 0.4
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 4243184 c.-49G>A upstream_gene_variant 0.2
embA 4243928 c.696C>A synonymous_variant 0.33
embA 4243958 c.726G>A synonymous_variant 0.4
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245110 p.Tyr626* stop_gained 0.33
embB 4246370 c.-144G>T upstream_gene_variant 0.18
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246745 p.Asp78Tyr missense_variant 0.5
embB 4246772 p.Val87Met missense_variant 0.5
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247810 p.Leu433Val missense_variant 0.29
aftB 4267009 p.Leu610Met missense_variant 0.17
aftB 4267591 p.Gln416Lys missense_variant 0.22
aftB 4267611 p.Asp409Gly missense_variant 0.2
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268506 c.331C>A synonymous_variant 0.5
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
ethR 4328177 p.Ser210Ile missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408422 c.-220T>C upstream_gene_variant 0.25