TB-Profiler result

Run: SRR8073606
Summary

Run ID: SRR8073606

Sample name:

Date: 04-04-2023 20:29:57

Number of reads: 3613599

Percentage reads mapped: 24.8

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 0.86 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 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
mshA 576105 p.Arg253Leu missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764751 p.Val461Gly missense_variant 0.25
rpoC 767305 p.Tyr1312* stop_gained 0.19
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.42
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.4
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.37
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.23
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.55
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.57
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.77
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.81
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.8
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.7
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.36
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.13
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.13
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.33
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.77
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.78
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.79
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.8
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.73
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.19
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.19
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.19
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.43
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.43
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.7
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.73
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.72
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.72
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.7
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.38
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.38
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.36
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.38
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.37
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.76
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.78
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.87
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.88
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.48
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.23
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.53
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.62
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.87
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.89
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.9
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.9
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.86
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.75
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.18
rrs 1472880 n.1035_1036insA non_coding_transcript_exon_variant 0.13
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.85
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.19
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.28
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.28
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.27
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.26
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.37
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.42
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.77
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.8
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.81
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.44
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.44
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.44
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.44
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.44
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.45
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.36
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.73
rrl 1473388 n.-270G>T upstream_gene_variant 0.16
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.21
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.51
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.44
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.46
rrl 1474255 n.598C>T non_coding_transcript_exon_variant 0.43
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.19
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.14
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.3
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.31
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.31
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.42
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.39
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.36
rrl 1474903 n.1246T>A non_coding_transcript_exon_variant 0.35
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.34
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.37
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.28
rrl 1475154 n.1497C>T non_coding_transcript_exon_variant 0.62
rrl 1475163 n.1506T>G non_coding_transcript_exon_variant 0.63
rrl 1475171 n.1514C>T non_coding_transcript_exon_variant 0.66
rrl 1475175 n.1518G>A non_coding_transcript_exon_variant 0.64
rrl 1475188 n.1531C>T non_coding_transcript_exon_variant 0.64
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.16
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.27
rrl 1475552 n.1895G>C non_coding_transcript_exon_variant 0.27
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.4
rrl 1475598 n.1941G>T non_coding_transcript_exon_variant 0.16
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.3
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.3
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.17
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.67
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.67
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.78
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.79
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.71
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.62
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.25
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.17
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.49
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.51
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.51
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.47
rrl 1476188 n.2531C>T non_coding_transcript_exon_variant 0.27
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.2
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.75
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.77
rrl 1476234 n.2577G>A non_coding_transcript_exon_variant 0.78
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.83
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.78
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.66
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.62
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.63
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.14
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.15
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.74
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.79
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.81
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.77
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.77
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.77
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.84
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.86
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.86
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.85
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.88
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.87
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.71
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.39
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.25
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.69
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.73
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.74
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.74
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.75
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.27
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.19
fabG1 1673449 p.Thr4Pro missense_variant 0.27
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.17
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
PPE35 2169320 p.Leu431Phe missense_variant 0.13
PPE35 2169866 c.747G>C synonymous_variant 0.18
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
kasA 2518144 c.30T>G synonymous_variant 0.14
eis 2715125 p.Thr70Ala missense_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.22
Rv2752c 3064741 p.Gly484Ala missense_variant 0.42
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
fbiD 3339153 p.Leu12Phe missense_variant 0.14
fbiD 3339273 c.156T>G synonymous_variant 0.18
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.23
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
fprA 3475280 p.Val425Gly missense_variant 0.29
fbiB 3641590 p.Gly19Glu missense_variant 1.0
alr 3841504 c.-84C>G upstream_gene_variant 0.21
rpoA 3878238 p.Asp90Glu missense_variant 0.19
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
embC 4241056 c.1194C>G synonymous_variant 0.19
embC 4241429 p.Phe523Val missense_variant 0.15
embC 4242476 p.Pro872Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.31
embA 4242970 c.-263C>T upstream_gene_variant 0.97
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
ubiA 4269529 p.Ala102Gly missense_variant 0.17
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