TB-Profiler result

Run: ERR4817463
Summary

Run ID: ERR4817463

Sample name:

Date: 01-04-2023 15:00:42

Number of reads: 5925483

Percentage reads mapped: 95.32

Strain: La3

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
La3 M.orygis None None 0.98
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.9 streptomycin
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 5516 p.Ile93Val missense_variant 0.98
gyrB 6109 c.870G>A synonymous_variant 0.99
gyrB 6446 p.Ala403Ser missense_variant 0.99
gyrB 6717 p.Ile493Thr missense_variant 0.96
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7775 c.474C>T synonymous_variant 0.96
gyrA 8930 c.1629C>T synonymous_variant 0.97
gyrA 9143 c.1842T>C synonymous_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 0.9
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491749 p.Leu323Phe missense_variant 0.98
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 0.86
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
mmpL5 778086 c.394dupG frameshift_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.2
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.2
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.2
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.2
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.78
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.79
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.79
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.86
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.89
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.89
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.93
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.93
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.87
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.97
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.91
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.89
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.86
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.5
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.38
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.87
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.86
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.89
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.89
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.89
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.88
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.84
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.59
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.22
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.18
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.19
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.24
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.12
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.12
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.11
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.12
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.12
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.11
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.11
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.16
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.16
rrl 1475539 n.1882A>G non_coding_transcript_exon_variant 1.0
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.33
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.29
rrl 1476239 n.2582T>C non_coding_transcript_exon_variant 0.18
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.31
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.31
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.31
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.29
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.27
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.43
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.4
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.15
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.35
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.65
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.6
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
rrl 1476664 n.3007T>G non_coding_transcript_exon_variant 0.94
inhA 1673680 c.-522C>G upstream_gene_variant 0.97
rpsA 1834363 c.822G>A synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154707 p.Val469Leu missense_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 1.0
PPE35 2170669 c.-57G>A upstream_gene_variant 0.96
Rv1979c 2222308 p.Asp286Gly missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289978 c.-737T>G upstream_gene_variant 0.96
kasA 2518132 c.18C>T synonymous_variant 0.98
ahpC 2726378 c.186T>A synonymous_variant 0.99
folC 2746391 p.Val403Ala missense_variant 0.94
Rv2752c 3067009 c.-818A>G upstream_gene_variant 0.97
thyX 3067812 p.Gln45Arg missense_variant 0.98
thyA 3074551 c.-80C>G upstream_gene_variant 0.5
ald 3086728 c.-92C>T upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.98
Rv3083 3448783 p.Val94Ile missense_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475113 c.1107G>A synonymous_variant 0.99
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475323 c.1317T>C synonymous_variant 0.94
Rv3236c 3612694 c.423T>C synonymous_variant 0.97
fbiB 3641584 p.Val17Ala missense_variant 0.97
clpC1 4039853 c.852G>A synonymous_variant 0.98
embC 4240671 p.Thr270Ile missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4244154 p.Thr308Ala missense_variant 0.96
embA 4244220 c.988C>T synonymous_variant 0.96
embB 4246864 c.351C>T synonymous_variant 0.99
embB 4247646 p.Glu378Ala missense_variant 0.97
aftB 4269351 c.-515C>T upstream_gene_variant 0.99
ubiA 4269387 p.Glu149Asp missense_variant 0.98
aftB 4269606 c.-770T>C upstream_gene_variant 0.99
ethA 4327042 p.Asp144Asn missense_variant 0.98
ethA 4328211 c.-738A>G upstream_gene_variant 0.98
whiB6 4338269 p.Gly85Ser missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407800 p.Val135Met missense_variant 0.97