TB-Profiler result

Run: ERR3439229
Summary

Run ID: ERR3439229

Sample name:

Date: 01-04-2023 01:58:12

Number of reads: 863172

Percentage reads mapped: 69.12

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 5789 p.Glu184Lys missense_variant 0.13
gyrB 5934 p.Ser232* stop_gained 0.18
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 8048 c.747C>A synonymous_variant 1.0
gyrA 8285 c.984C>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 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776032 p.Gly817Arg missense_variant 0.23
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778327 p.Gln52Lys missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801454 p.Glu216Gln missense_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303380 c.450T>C synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471935 n.90T>C non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.5
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.67
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.33
rrl 1474629 n.972G>A non_coding_transcript_exon_variant 0.67
rrl 1474768 n.1111C>G non_coding_transcript_exon_variant 0.29
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.62
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.62
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.56
rrl 1474801 n.1144G>C non_coding_transcript_exon_variant 0.5
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.44
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.56
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.56
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.56
rrl 1474826 n.1169T>A non_coding_transcript_exon_variant 0.44
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.56
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.56
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.62
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.6
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.71
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.71
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.71
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.71
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.6
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.6
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.4
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.5
rrl 1475752 n.2095C>A non_coding_transcript_exon_variant 0.5
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.5
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.4
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.4
rrl 1475776 n.2119G>T non_coding_transcript_exon_variant 0.4
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.4
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.4
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.4
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.4
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.4
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.4
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.4
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.67
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.83
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.86
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.86
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.71
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.86
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.86
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.83
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.83
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.86
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.9
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.9
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.62
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.19
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.11
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.79
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.53
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.73
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.43
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.53
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.47
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.41
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.12
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.21
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.44
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.5
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.4
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.4
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.4
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.4
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.4
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.4
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.4
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.5
inhA 1673715 c.-487C>G upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154085 p.Gly676Val missense_variant 0.22
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 2169689 c.924C>T synonymous_variant 0.18
PPE35 2170678 c.-66C>A upstream_gene_variant 0.13
Rv1979c 2221893 c.1272C>A synonymous_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222354 p.Leu271Ile missense_variant 0.2
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
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
clpC1 4039927 p.Arg260Ser missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242642 p.Arg927His 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 4248734 p.Arg741Trp missense_variant 1.0
aftB 4267167 p.Gln557Pro 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
ethA 4326024 p.Pro484Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0