TB-Profiler result

Run: ERR4769428
Summary

Run ID: ERR4769428

Sample name:

Date: 01-04-2023 06:40:12

Number of reads: 269993

Percentage reads mapped: 13.51

Strain: La1.3

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
La1.3 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
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7054 c.-248C>T upstream_gene_variant 0.13
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761466 c.1660C>T synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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
rpsL 781586 c.27C>A synonymous_variant 0.17
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303894 p.Arg322Trp missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.25
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.25
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.3
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.3
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.27
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.33
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.7
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.7
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.71
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.73
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.73
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.73
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.76
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.84
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.84
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.84
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.84
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.9
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.95
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.87
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.85
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.85
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.85
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.85
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.83
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.83
rrs 1472679 n.834_835insAC non_coding_transcript_exon_variant 0.83
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.81
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.78
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.78
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.78
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.78
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.78
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.78
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.8
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.8
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.79
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.68
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.29
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.27
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.25
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.2
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.14
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.8
rrs 1472953 n.1108_1109insA non_coding_transcript_exon_variant 0.96
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.96
rrs 1472958 n.1114delT non_coding_transcript_exon_variant 0.96
rrs 1472970 n.1125C>A non_coding_transcript_exon_variant 0.97
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.96
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.96
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.95
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.94
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.95
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.95
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.96
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.89
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.89
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.88
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.85
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.83
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.33
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.25
rrl 1474758 n.1101G>A non_coding_transcript_exon_variant 0.33
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.7
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.7
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.7
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.75
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.79
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.83
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.84
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.86
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.86
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.85
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.84
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.88
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.91
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.86
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.86
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.78
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.69
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 0.5
rrl 1475122 n.1465C>T non_coding_transcript_exon_variant 0.4
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.4
rrl 1475154 n.1497C>A non_coding_transcript_exon_variant 0.6
rrl 1475167 n.1510T>A non_coding_transcript_exon_variant 0.75
rrl 1475672 n.2015C>G non_coding_transcript_exon_variant 0.25
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.25
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.3
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.36
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.36
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.36
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.36
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.4
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.3
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.3
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.27
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.27
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.6
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.6
rrl 1476181 n.2524A>C non_coding_transcript_exon_variant 0.6
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.56
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.56
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.56
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.56
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.56
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.56
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.56
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.56
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.56
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.56
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.56
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.67
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.78
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.83
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.87
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.87
rrl 1476269 n.2612C>G non_coding_transcript_exon_variant 0.84
rrl 1476274 n.2617G>C non_coding_transcript_exon_variant 0.84
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.84
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.87
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.87
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.87
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.87
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.87
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.87
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.87
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.85
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.85
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.86
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.91
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.92
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.93
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.94
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.94
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.94
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.93
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.9
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.95
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.96
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.93
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.95
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.85
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.76
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.75
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.75
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.75
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.75
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.75
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.75
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.75
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.81
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.84
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.81
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.81
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.77
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.54
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.22
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.22
rrl 1476728 n.3071T>C non_coding_transcript_exon_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102466 p.Ala193Thr missense_variant 0.25
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154040 p.Gly691Asp 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
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg 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 2714273 p.Asp354Asn missense_variant 0.17
thyX 3067887 p.Pro20Gln missense_variant 0.25
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
embC 4241384 p.Pro508Thr 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
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 4249640 c.3127T>C synonymous_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268100 p.Ala246Glu missense_variant 0.17
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
ethR 4327943 p.Val132Asp missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407908 p.Glu99Lys missense_variant 0.25
gid 4408195 p.Pro3Leu missense_variant 0.17