TB-Profiler result

Run: ERR4821773
Summary

Run ID: ERR4821773

Sample name:

Date: 01-04-2023 17:26:39

Number of reads: 2489056

Percentage reads mapped: 84.87

Strain: La1.6

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
La1.6 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 0.73 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 5724 p.Ala162Val missense_variant 1.0
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 7042 c.-260C>T upstream_gene_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
rpoB 762026 c.2220G>C synonymous_variant 0.12
rpoB 762053 c.2247T>C synonymous_variant 0.13
rpoB 762057 p.Ile751Val missense_variant 0.13
rpoB 762062 c.2256T>C synonymous_variant 0.14
rpoB 762065 c.2259T>C synonymous_variant 0.15
rpoB 762071 p.Asp755Glu missense_variant 0.15
rpoB 762080 c.2274G>C synonymous_variant 0.16
rpoB 762085 p.Ala760Glu missense_variant 0.15
rpoB 762089 c.2283G>A synonymous_variant 0.15
rpoB 762110 c.2304G>C synonymous_variant 0.15
rpoB 762245 c.2439G>C synonymous_variant 0.1
rpoB 762254 c.2448T>C synonymous_variant 0.12
rpoB 762275 c.2469C>T synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763708 c.339G>C synonymous_variant 0.14
rpoC 763714 c.345G>C synonymous_variant 0.12
rpoC 763717 c.348T>C synonymous_variant 0.12
rpoC 763718 p.Leu117Val missense_variant 0.11
rpoC 763723 c.354G>C synonymous_variant 0.12
rpoC 763724 p.Asp119Asn missense_variant 0.12
rpoC 763729 c.360G>C synonymous_variant 0.12
rpoC 763732 c.363C>G synonymous_variant 0.12
rpoC 763735 c.366G>C synonymous_variant 0.11
rpoC 763744 c.375G>C synonymous_variant 0.11
rpoC 763751 p.Ile128Val missense_variant 0.12
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
embR 1416489 p.Gln287* stop_gained 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.18
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.41
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.44
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.44
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.48
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.58
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.62
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.66
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.86
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.77
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.33
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.25
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.2
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.18
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.18
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.17
rrs 1472427 n.582T>G non_coding_transcript_exon_variant 0.17
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.64
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.18
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.5
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.61
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.68
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.71
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.8
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.76
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.91
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.79
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.79
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.82
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.13
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.75
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.7
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.67
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.56
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.5
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.57
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.57
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.67
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.67
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.7
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.17
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.77
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.18
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.78
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.69
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.69
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.68
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.26
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.68
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.67
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.78
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.24
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.41
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.71
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.44
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.65
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.68
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.68
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.76
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.75
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.76
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.81
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.78
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.73
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.73
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.69
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.56
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.56
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.61
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.57
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.47
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.47
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.46
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.46
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.41
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.44
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.55
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.56
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.51
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.51
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.1
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.67
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.83
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.76
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.67
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.67
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.52
rrs 1473289 n.1444_1445insTTTTG non_coding_transcript_exon_variant 0.56
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.56
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.53
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.55
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.6
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.75
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 1.0
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.4
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.4
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.82
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.44
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 0.67
rrl 1475673 n.2021delA non_coding_transcript_exon_variant 0.67
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.83
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.89
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.89
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.84
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 0.84
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.84
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.33
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.33
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.25
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.33
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.33
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.33
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.33
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.4
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.56
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.44
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.4
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.5
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.57
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.59
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.68
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.71
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.8
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.72
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918536 c.597T>C synonymous_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 2223062 p.Thr35Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
folC 2746245 p.Ala452Thr missense_variant 1.0
ribD 2987615 c.777A>G stop_lost&splice_region_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
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 4243763 c.531G>C synonymous_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 0.99
embB 4246663 c.150G>A synonymous_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4246974 p.His154Arg missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.99
embB 4247791 c.1278C>T synonymous_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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0