TB-Profiler result

Run: ERR5311087
Summary

Run ID: ERR5311087

Sample name:

Date: 01-04-2023 22:30:42

Number of reads: 1111213

Percentage reads mapped: 27.35

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 0.99
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 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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.12
rpoC 764405 c.1036A>C synonymous_variant 0.13
rpoC 764428 c.1059G>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.19
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.14
rpoC 764443 p.Ile358Met missense_variant 0.14
rpoC 764446 p.Asp359Glu missense_variant 0.15
rpoC 764450 p.Gly361Arg missense_variant 0.14
rpoC 764461 p.Glu364Asp missense_variant 0.2
rpoC 764471 p.Asn368Arg missense_variant 0.16
rpoC 764479 c.1110G>A synonymous_variant 0.2
rpoC 764485 c.1116G>C synonymous_variant 0.23
rpoC 764498 p.Ser377Ala missense_variant 0.26
rpoC 764503 c.1134G>C synonymous_variant 0.36
rpoC 764527 c.1158C>T synonymous_variant 0.38
rpoC 764536 c.1167G>C synonymous_variant 0.33
rpoC 764537 p.Pro390Thr missense_variant 0.29
rpoC 764540 p.Val391Ile missense_variant 0.29
rpoC 764545 c.1176C>G synonymous_variant 0.28
rpoC 764548 c.1179G>C synonymous_variant 0.27
rpoC 764549 p.Pro394Ala missense_variant 0.28
rpoC 764552 p.Gly395Asn missense_variant 0.28
rpoC 764557 p.Asn396Lys missense_variant 0.28
rpoC 764575 c.1206T>G synonymous_variant 0.32
rpoC 764581 c.1212T>C synonymous_variant 0.34
rpoC 764582 p.Leu405Met missense_variant 0.31
rpoC 764587 c.1218C>G synonymous_variant 0.34
rpoC 764605 c.1236G>C synonymous_variant 0.32
rpoC 764611 c.1242G>T synonymous_variant 0.31
rpoC 764632 c.1263T>C synonymous_variant 0.27
rpoC 764641 c.1272C>T synonymous_variant 0.24
rpoC 764650 c.1281G>T synonymous_variant 0.2
rpoC 764664 p.Val432Ala missense_variant 0.12
rpoC 764672 p.Gln435Glu missense_variant 0.12
rpoC 764677 c.1308C>G synonymous_variant 0.13
rpoC 764695 c.1326T>C synonymous_variant 0.16
rpoC 764701 c.1332C>G synonymous_variant 0.12
rpoC 764716 c.1347G>C synonymous_variant 0.18
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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
atpE 1461051 p.Pro3Thr missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 1.0
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.67
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.67
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.75
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.75
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.5
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.5
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.5
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.5
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.4
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.4
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.4
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.4
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
rpsA 1834166 p.Gly209Arg missense_variant 1.0
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 2167991 c.2622C>T synonymous_variant 0.18
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
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
Rv2752c 3064848 c.1344C>T synonymous_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
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
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
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
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
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408237 c.-35C>A upstream_gene_variant 1.0