TB-Profiler result

Run: ERR3439225
Summary

Run ID: ERR3439225

Sample name:

Date: 01-04-2023 01:57:41

Number of reads: 805379

Percentage reads mapped: 66.57

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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.29 streptomycin
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776033 c.2448C>T synonymous_variant 0.15
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
fbiC 1305360 c.2430G>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.5
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.5
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.67
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.67
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.67
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.67
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.4
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.4
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.4
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.4
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.4
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.33
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.29
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.29
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.29
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.33
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.29
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.29
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.29
rrs 1472439 n.594C>A non_coding_transcript_exon_variant 0.33
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.55
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.27
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.3
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.25
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.3
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.4
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.5
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.2
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.5
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.29
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.38
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.3
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.43
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.22
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.2
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 0.25
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.25
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.4
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.33
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.29
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.29
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.29
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.29
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.29
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.4
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.6
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.6
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.4
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.5
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.4
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.4
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.4
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.4
rrl 1475752 n.2095C>A non_coding_transcript_exon_variant 0.4
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.4
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.33
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.29
rrl 1475776 n.2119G>T non_coding_transcript_exon_variant 0.25
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.2
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.2
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.2
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.2
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.17
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.6
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.71
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.5
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.4
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.5
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.4
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.6
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.6
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.6
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.75
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.5
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.75
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.6
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.6
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.4
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.69
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.2
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.65
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.18
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.89
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.19
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.9
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.71
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.83
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.58
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.18
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.23
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.56
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.79
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.62
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.42
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.2
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.19
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.19
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.2
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.56
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.62
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.29
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.29
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.4
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.29
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.29
rpsA 1834166 p.Gly209Arg missense_variant 0.67
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 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
eis 2715328 p.Thr2Ile missense_variant 0.18
Rv2752c 3065830 p.Ile121Thr missense_variant 0.17
thyA 3073755 c.717C>T synonymous_variant 0.3
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 0.93
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 4039570 c.1132_1134delGCG conservative_inframe_deletion 0.18
clpC1 4040604 p.Leu34Pro missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242680 p.Ala940Ser missense_variant 0.5
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 4269495 c.-659G>A upstream_gene_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327530 c.-57G>A upstream_gene_variant 0.31
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 0.32