TB-Profiler result

Run: ERR6201843
Summary

Run ID: ERR6201843

Sample name:

Date: 02-04-2023 01:53:07

Number of reads: 1195909

Percentage reads mapped: 20.22

Strain: La1.2

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
La1.2 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
gid 4407851 c.351delG frameshift_variant 0.12 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 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
gyrB 6728 p.Leu497Val missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7821 c.520C>T synonymous_variant 1.0
gyrA 8273 c.972C>G synonymous_variant 0.11
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575717 p.Asp124Tyr missense_variant 0.14
mshA 575978 p.Asp211Tyr missense_variant 0.22
rpoC 762803 c.-567C>T upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764135 p.Met256Leu missense_variant 0.14
rpoC 764659 c.1290C>T synonymous_variant 0.17
rpoC 765751 c.2382C>A synonymous_variant 0.13
rpoC 766366 c.2997C>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776643 p.Met613Thr missense_variant 0.11
mmpS5 778671 p.Gln79* stop_gained 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781683 p.Pro42Ala missense_variant 0.14
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303077 c.147C>A synonymous_variant 0.22
fbiC 1303539 c.609G>A synonymous_variant 0.13
Rv1258c 1406578 p.Gln255* stop_gained 0.14
Rv1258c 1406663 c.678C>T synonymous_variant 1.0
atpE 1461225 p.Glu61* stop_gained 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.2
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.21
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.19
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.18
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.51
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.51
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.79
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.85
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.88
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.88
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.89
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.9
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.9
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.9
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.91
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.92
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.92
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.9
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.9
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.89
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.89
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.91
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.89
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.89
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.9
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.84
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.78
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.73
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.64
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.41
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.4
rrs 1472277 n.432C>A non_coding_transcript_exon_variant 0.16
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.24
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.25
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.24
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.24
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.24
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.12
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.39
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.72
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.85
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.85
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.85
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.83
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.86
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.86
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.88
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.89
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.88
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.89
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.9
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.9
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.9
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.91
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.92
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.92
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.93
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.92
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.89
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.89
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.95
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.9
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.91
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.88
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.89
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.84
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.84
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.76
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.63
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.56
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.49
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.25
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.19
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.24
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.69
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.64
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.64
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.64
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.64
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.63
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.62
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.64
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.63
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.64
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.63
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.64
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.64
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.64
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.64
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.65
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.69
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.69
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.76
rrl 1474723 n.1066G>T non_coding_transcript_exon_variant 0.14
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.3
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.3
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.35
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.35
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.35
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.29
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.24
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.17
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.17
rrl 1474981 n.1324G>A non_coding_transcript_exon_variant 0.15
rrl 1475370 n.1713G>T non_coding_transcript_exon_variant 0.14
rrl 1475375 n.1718G>T non_coding_transcript_exon_variant 0.15
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.33
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.32
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.36
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.35
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.32
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.3
rrl 1475895 n.2238C>G non_coding_transcript_exon_variant 0.13
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.25
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.33
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.31
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.38
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.3
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.36
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.92
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.94
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.95
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.95
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.95
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.94
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.94
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.94
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.94
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.94
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.94
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.94
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.94
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.93
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.94
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.95
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.95
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.95
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.96
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.97
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.97
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.97
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.97
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.97
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.97
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.97
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.98
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.98
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.98
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.98
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.98
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.96
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.96
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.94
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.94
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.95
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.95
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.94
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.94
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.94
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.94
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.94
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.95
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.94
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.93
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.92
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.88
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.27
inhA 1674266 p.Ala22Glu missense_variant 0.18
rpsA 1833422 c.-120G>T upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
rpsA 1834919 p.Ala460Thr missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102035 c.1008C>A synonymous_variant 0.13
ndh 2102106 p.Gly313Arg 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
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167763 c.2850A>T synonymous_variant 0.18
PPE35 2167811 c.2801delA frameshift_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167999 p.Pro872Thr missense_variant 0.22
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168364 p.Thr750Lys missense_variant 0.13
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170062 p.Ala184Gly missense_variant 0.33
PPE35 2170065 p.Ala183Gly missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289694 c.-453G>T upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
folC 2746962 p.Ala213Ser missense_variant 0.14
pepQ 2860159 p.Ala87Gly missense_variant 0.33
ribD 2986843 p.Pro2Leu missense_variant 0.2
ribD 2986852 p.Gly5Asp missense_variant 0.15
ribD 2986876 p.Pro13Gln missense_variant 0.15
Rv2752c 3066033 c.159C>T synonymous_variant 0.13
thyX 3067786 p.Thr54Ala 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
fbiD 3339154 p.Ile13Leu missense_variant 1.0
Rv3083 3448400 c.-104G>A upstream_gene_variant 0.13
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449675 p.Thr391Ser missense_variant 0.11
Rv3083 3449984 p.Ala494Glu missense_variant 0.12
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
Rv3236c 3612840 p.Ala93Pro missense_variant 0.18
fbiA 3641024 p.Asp161Gly missense_variant 0.12
fbiA 3641149 p.Leu203Met missense_variant 0.15
fbiB 3641913 p.Ala127Ser missense_variant 0.17
rpoA 3878257 p.Val84Ala missense_variant 0.14
rpoA 3878299 p.Lys70Arg missense_variant 0.17
clpC1 4038320 c.2385G>A synonymous_variant 0.18
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244792 c.1560G>C synonymous_variant 0.22
embA 4245433 p.Ala734Val missense_variant 0.17
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246760 p.Val83Leu missense_variant 0.12
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248051 p.Gly513Glu missense_variant 0.13
embB 4248319 c.1806A>C synonymous_variant 0.15
embB 4249431 p.Ser973Leu missense_variant 0.2
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4267981 p.Arg286Trp missense_variant 0.13
aftB 4268491 p.Ile116Phe missense_variant 0.25
aftB 4268639 c.198G>T synonymous_variant 0.5
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0