TB-Profiler result

Run: ERR5311092
Summary

Run ID: ERR5311092

Sample name:

Date: 01-04-2023 22:30:52

Number of reads: 646072

Percentage reads mapped: 26.25

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 5813 p.Arg192Cys missense_variant 0.15
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 7988 c.687G>A synonymous_variant 0.14
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
rpoB 762867 p.Tyr1021His missense_variant 0.17
rpoB 763029 p.Ala1075Thr missense_variant 0.22
rpoC 764605 c.1236G>C synonymous_variant 0.13
rpoC 764611 c.1242G>T synonymous_variant 0.12
rpoC 764632 c.1263T>C synonymous_variant 0.14
rpoC 764641 c.1272C>T synonymous_variant 0.15
rpoC 764650 c.1281G>T synonymous_variant 0.14
rpoC 764668 c.1299C>T synonymous_variant 0.15
rpoC 764672 p.Gln435Glu missense_variant 0.15
rpoC 764677 c.1308C>G synonymous_variant 0.15
rpoC 764695 c.1326T>C synonymous_variant 0.18
rpoC 764705 p.Leu446Lys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775711 p.Phe924Leu missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779199 p.Asn70Lys missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304720 p.Thr597Ile missense_variant 0.12
fbiC 1304729 p.Cys600Tyr missense_variant 0.14
Rv1258c 1406081 c.1260A>G stop_lost&splice_region_variant 0.93
embR 1416496 c.852G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.67
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.67
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.67
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.5
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.5
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.4
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.4
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.4
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.5
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.5
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.5
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.5
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.5
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.5
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.5
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.4
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.4
rrl 1475159 n.1502G>A non_coding_transcript_exon_variant 0.67
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.5
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.67
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rpsA 1834017 p.Arg159Leu missense_variant 0.12
rpsA 1834166 p.Gly209Cys missense_variant 0.18
rpsA 1834241 c.700C>T synonymous_variant 0.17
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 2154703 p.Ser470* stop_gained 0.33
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
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223312 c.-148C>A upstream_gene_variant 0.2
pncA 2289974 c.-733G>A upstream_gene_variant 0.13
kasA 2518112 c.-3C>T upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
eis 2715211 p.Pro41His missense_variant 0.12
folC 2746245 p.Ala452Thr missense_variant 0.2
folC 2747467 c.132T>C synonymous_variant 0.22
folC 2747652 c.-54G>A upstream_gene_variant 0.14
folC 2747721 c.-123C>A upstream_gene_variant 0.2
pepQ 2860564 c.-146A>G upstream_gene_variant 0.15
ribD 2987284 p.Ala149Val missense_variant 0.12
Rv2752c 3066321 c.-130C>T upstream_gene_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
Rv3083 3448783 p.Val94Ile missense_variant 1.0
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
fbiB 3641175 c.-360G>C upstream_gene_variant 0.1
fbiB 3642580 p.Ile349Lys missense_variant 0.12
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4239989 c.127C>T synonymous_variant 0.13
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
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 4248377 c.1868_1869delGC frameshift_variant 0.17
embB 4248962 p.Ala817Ser 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
ubiA 4269433 p.Met134Thr missense_variant 0.17
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327373 p.Ile34Asn missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0