TB-Profiler result

Run: SRR8600207
Summary

Run ID: SRR8600207

Sample name:

Date: 04-04-2023 21:38:29

Number of reads: 1319668

Percentage reads mapped: 99.45

Strain: La1.8.1

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
La1.8 M.bovis None None 1.0
La1.8.1 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
gyrB 6620 p.Asp461His missense_variant 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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
gyrB 6086 p.Thr283Ser missense_variant 0.25
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 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
gyrA 9569 c.2268C>T synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575171 c.-177C>T upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764386 c.1017C>T synonymous_variant 0.15
rpoC 766335 p.Val989Ala missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778301 p.Gln60His missense_variant 0.14
mmpL5 778392 p.Thr30Asn missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304357 p.Ile476Thr missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471698 n.-148A>G upstream_gene_variant 0.13
rrs 1472064 n.219G>A non_coding_transcript_exon_variant 0.13
rrs 1472480 n.635G>T non_coding_transcript_exon_variant 0.2
rrl 1475750 n.2093A>C non_coding_transcript_exon_variant 1.0
rrl 1475919 n.2262C>A non_coding_transcript_exon_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
rpsA 1834183 c.642T>C synonymous_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917874 c.-66G>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102097 p.Asn316Asp missense_variant 0.12
ndh 2102193 p.Arg284Trp 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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168010 p.Ser868Pro missense_variant 0.25
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2168876 p.Phe579Leu missense_variant 0.18
PPE35 2168896 p.Gly573Cys missense_variant 0.25
PPE35 2169394 p.Ala407Ser missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2221891 p.Ser425Leu missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222659 c.503_505delTAG disruptive_inframe_deletion 0.17
Rv1979c 2222941 p.Asn75Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
eis 2715205 p.Asp43Val missense_variant 0.12
Rv2752c 3065988 p.Glu68Asp missense_variant 1.0
Rv2752c 3066301 c.-110G>A upstream_gene_variant 0.13
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
Rv3083 3449576 p.Leu358His missense_variant 0.17
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
Rv3236c 3612189 p.Met310Val missense_variant 0.11
fbiA 3640466 c.-77T>C upstream_gene_variant 0.17
alr 3841033 p.Val130Ile missense_variant 0.22
rpoA 3877636 p.Gln291Leu missense_variant 0.2
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
embA 4244594 c.1362G>A synonymous_variant 0.14
embB 4246551 p.Asn13Ser missense_variant 0.8
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248054 p.Pro514Gln missense_variant 0.14
embB 4248317 p.Val602Pro missense_variant 0.17
embB 4248321 p.Gly603Ala missense_variant 0.17
aftB 4267846 p.Gly331Ser missense_variant 0.22
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
ethA 4326504 p.Gly324* stop_gained 0.18
ethA 4327241 p.Gly78Asp missense_variant 0.14
whiB6 4338576 c.-55G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0