TB-Profiler result

Run: ERR3439279
Summary

Run ID: ERR3439279

Sample name:

Date: 01-04-2023 02:01:08

Number of reads: 97757

Percentage reads mapped: 9.18

Strain: lineage4.9;La1.8

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 0.12
La1.8 M.bovis None None 0.18
lineage4.9 Euro-American (H37Rv-like) T1 None 0.88
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 0.6 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
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 0.67
gyrA 8927 p.Lys542Asn missense_variant 0.67
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620563 p.Leu225Met missense_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781763 c.204C>A synonymous_variant 0.4
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.6
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.5
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.5
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.67
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.5
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.6
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.5
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.5
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.6
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.6
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.6
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.6
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.8
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.6
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.6
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.29
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.71
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.33
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.17
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.33
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.73
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.92
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.71
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.71
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.38
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.31
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.62
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.92
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.8
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.89
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.69
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.55
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.25
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.25
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.24
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.24
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.53
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.91
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.86
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.83
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.8
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.67
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.8
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.8
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.8
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.8
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.8
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.8
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.8
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.75
inhA 1674955 p.Ala252Thr missense_variant 0.5
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917926 c.-14G>T upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp missense_variant 0.67
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714653 p.Arg227Leu missense_variant 0.67
ahpC 2726441 c.249G>T synonymous_variant 1.0
thyX 3067592 c.354G>T synonymous_variant 0.67
ald 3086728 c.-92C>T upstream_gene_variant 1.0
fbiD 3339515 p.Arg133Leu missense_variant 0.4
fbiD 3339666 c.549G>T synonymous_variant 0.4
fbiD 3339734 p.Ala206Val missense_variant 0.4
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448988 p.Arg162Gln missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612141 p.Ala326Thr missense_variant 0.67
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
panD 4044386 c.-105C>A upstream_gene_variant 0.5
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245676 p.Gly815Val missense_variant 0.4
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 4248734 p.Arg741Trp missense_variant 0.5
gid 4407588 c.615A>G synonymous_variant 1.0