TB-Profiler result

Run: SRR8600107
Summary

Run ID: SRR8600107

Sample name:

Date: 04-04-2023 21:34:05

Number of reads: 627225

Percentage reads mapped: 96.13

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
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 6210 p.Leu324Pro missense_variant 0.11
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 8094 p.Gly265Cys missense_variant 0.12
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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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
rplC 800970 p.Tyr54* stop_gained 0.12
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303087 p.Asp53Tyr missense_variant 0.15
fbiC 1304542 p.Asp538Tyr missense_variant 0.15
fbiC 1304833 p.Pro635Thr missense_variant 0.17
Rv1258c 1406751 p.Gly197Asp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.17
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.15
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.15
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.15
rrl 1474269 n.612C>A non_coding_transcript_exon_variant 0.15
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.15
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.17
rrl 1474287 n.631_649delCCTTTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.2
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.15
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.18
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.18
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.11
rrl 1474752 n.1095T>C non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.1
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.11
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.12
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.13
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.13
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.13
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1475427 n.1770C>T non_coding_transcript_exon_variant 0.22
rrl 1476041 n.2384A>G non_coding_transcript_exon_variant 0.18
rrl 1476322 n.2665C>A non_coding_transcript_exon_variant 0.2
rrl 1476707 n.3050C>A non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
rpsA 1834772 p.Arg411Ser missense_variant 0.15
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
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 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 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289401 c.-161delT upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.2
ribD 2986789 c.-50A>T upstream_gene_variant 0.11
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 3448684 p.Thr61Ser missense_variant 0.15
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449478 c.975C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474445 p.Gly147Cys missense_variant 0.13
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3641497 p.Met319Val missense_variant 0.1
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040499 p.Gln69Arg missense_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241232 p.Arg457Gln missense_variant 0.15
embC 4241689 c.1827G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242680 p.Ala940Ser missense_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 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248445 c.1932C>T synonymous_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268880 c.-44C>T upstream_gene_variant 0.12
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