TB-Profiler result

Run: ERR4187604
Summary

Run ID: ERR4187604

Sample name:

Date: 01-04-2023 04:38:41

Number of reads: 357440

Percentage reads mapped: 35.93

Strain: La1.8.1

Drug-resistance: RR-TB

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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 0.96
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
rpoB 761086 p.Thr427Ser missense_variant 0.33 rifampicin
rpoB 761116 p.Asn437Thr missense_variant 0.2 rifampicin
rpoB 761127 p.Ser441Ala missense_variant 0.22 rifampicin
rpoB 761131 p.Gly442Glu missense_variant 0.25 rifampicin
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
rpoB 761027 c.1221A>G synonymous_variant 0.25
rpoB 761034 p.Thr410Ala missense_variant 0.25
rpoB 761048 c.1242C>T synonymous_variant 0.25
rpoB 761051 c.1245G>T synonymous_variant 0.25
rpoB 761058 p.Val418Ile missense_variant 0.25
rpoB 761063 c.1257C>T synonymous_variant 0.25
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.33
rpoB 761096 c.1290G>C synonymous_variant 0.29
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.29
rpoB 761102 c.1296A>G synonymous_variant 0.29
rpoB 761133 c.1327T>C synonymous_variant 0.25
rpoB 761138 c.1332C>G synonymous_variant 0.25
rpoB 761150 c.1344A>T synonymous_variant 0.22
rpoB 761156 c.1350G>C synonymous_variant 0.22
rpoB 761162 c.1356G>C synonymous_variant 0.22
rpoB 761165 c.1359G>T synonymous_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766534 c.3165C>A synonymous_variant 0.67
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 1471896 n.51T>C non_coding_transcript_exon_variant 0.5
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.5
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.5
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.7
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.86
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.86
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.86
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.91
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.91
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.95
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.96
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.96
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.95
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.95
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.95
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.67
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.57
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.9
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.9
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.9
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.9
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.9
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.9
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.92
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.93
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.93
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.93
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.93
rrs 1472669 n.824_825insTGG non_coding_transcript_exon_variant 0.89
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.84
rrs 1472681 n.838_843delTGGGAT non_coding_transcript_exon_variant 0.84
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.84
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.84
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.85
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.8
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.81
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.9
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.9
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.9
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.9
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.91
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.75
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.6
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.84
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.83
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.83
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.83
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.83
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.83
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.83
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.83
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.83
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.83
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.88
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.88
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.88
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.88
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.88
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.88
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.88
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.88
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.89
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.92
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.91
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.86
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.8
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.67
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.67
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 1.0
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 1.0
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 1.0
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 1.0
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 1.0
rrl 1474910 n.1253C>G non_coding_transcript_exon_variant 1.0
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 1.0
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 1.0
rrl 1475129 n.1472G>T non_coding_transcript_exon_variant 1.0
rrl 1475144 n.1487G>C non_coding_transcript_exon_variant 0.6
rrl 1475145 n.1488C>T non_coding_transcript_exon_variant 0.6
rrl 1475154 n.1497C>A non_coding_transcript_exon_variant 0.6
rrl 1475163 n.1506T>G non_coding_transcript_exon_variant 0.6
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.75
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.75
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.75
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.75
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 1.0
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 1.0
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 1.0
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 1.0
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 1.0
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 1.0
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 1.0
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.95
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.96
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.96
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 0.94
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 0.97
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.97
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.98
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.98
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.96
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.96
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.98
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.99
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 1.0
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 1.0
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 1.0
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 1.0
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 1.0
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 1.0
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 1.0
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 1.0
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 1.0
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 1.0
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 1.0
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.97
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.93
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.93
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.88
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.85
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.85
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.82
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.75
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 2714555 p.Asp260Asn missense_variant 0.29
eis 2715125 p.Thr70Ala missense_variant 1.0
thyX 3067695 p.Gly84Glu missense_variant 0.25
thyA 3073755 c.717C>T synonymous_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
embC 4242680 p.Ala940Ser missense_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
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
ethA 4327530 c.-57G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0