TB-Profiler result

Run: ERR4188222
Summary

Run ID: ERR4188222

Sample name:

Date: 01-04-2023 04:58:02

Number of reads: 422777

Percentage reads mapped: 29.57

Strain: La1.8.1

Drug-resistance: MDR-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 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
rpoB 761196 p.Leu464Met missense_variant 0.2 rifampicin
katG 2154569 p.Arg515Cys missense_variant 0.33 isoniazid
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 5172 c.-68C>T upstream_gene_variant 0.2
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 0.88
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
mshA 576217 c.870G>A synonymous_variant 0.2
rpoB 761138 c.1332C>G synonymous_variant 0.29
rpoB 761150 c.1344A>T synonymous_variant 0.22
rpoB 761162 c.1356G>C synonymous_variant 0.2
rpoB 761165 c.1359G>T synonymous_variant 0.18
rpoB 761168 c.1362C>G synonymous_variant 0.18
rpoB 761178 p.Ser458Thr missense_variant 0.2
rpoB 761183 c.1377T>G synonymous_variant 0.2
rpoB 761186 c.1380G>A synonymous_variant 0.2
rpoB 761189 c.1383T>C synonymous_variant 0.2
rpoB 761192 c.1386C>G synonymous_variant 0.2
rpoB 761195 c.1389G>C synonymous_variant 0.2
rpoB 761201 c.1395G>A synonymous_variant 0.2
rpoB 761213 c.1407G>C synonymous_variant 0.18
rpoB 761216 c.1410C>T synonymous_variant 0.18
rpoB 761222 c.1416G>C synonymous_variant 0.17
rpoB 761249 c.1443A>G synonymous_variant 0.14
rpoB 761252 c.1446C>G synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.44
rpoC 764410 c.1041G>C synonymous_variant 0.33
rpoC 764419 c.1050C>G synonymous_variant 0.28
rpoC 764428 c.1059G>T synonymous_variant 0.27
rpoC 764434 c.1065A>G synonymous_variant 0.26
rpoC 764435 c.1066_1068delAGGinsCGT synonymous_variant 0.26
rpoC 764440 c.1071G>T synonymous_variant 0.26
rpoC 764441 p.Ile358Leu missense_variant 0.26
rpoC 764446 c.1077T>C synonymous_variant 0.24
rpoC 764452 c.1083T>C synonymous_variant 0.25
rpoC 764461 p.Glu364Asp missense_variant 0.26
rpoC 764470 c.1101C>A synonymous_variant 0.23
rpoC 764471 p.Asn368Gln missense_variant 0.23
rpoC 764494 c.1125G>A synonymous_variant 0.35
rpoC 764498 p.Ser377Ala missense_variant 0.35
rpoC 764503 c.1134G>C synonymous_variant 0.34
rpoC 764513 p.Phe382Ile missense_variant 0.34
rpoC 764521 c.1152T>C synonymous_variant 0.36
rpoC 764527 c.1158C>T synonymous_variant 0.36
rpoC 764536 c.1167G>T synonymous_variant 0.3
rpoC 764539 c.1170C>G synonymous_variant 0.27
rpoC 764545 c.1176C>G synonymous_variant 0.25
rpoC 764548 c.1179G>C synonymous_variant 0.27
rpoC 764551 c.1182G>C synonymous_variant 0.28
rpoC 764569 c.1200G>A synonymous_variant 0.3
rpoC 764575 c.1206T>C synonymous_variant 0.31
rpoC 764576 c.1207_1208delTCinsAG synonymous_variant 0.31
rpoC 764579 p.Asp404His missense_variant 0.31
rpoC 764582 p.Leu405Met missense_variant 0.31
rpoC 764587 c.1218C>G synonymous_variant 0.38
rpoC 764599 c.1230G>A synonymous_variant 0.42
rpoC 764605 c.1236G>C synonymous_variant 0.43
rpoC 764611 c.1242G>T synonymous_variant 0.42
rpoC 764632 c.1263T>C synonymous_variant 0.36
rpoC 764644 c.1275G>C synonymous_variant 0.26
rpoC 764650 c.1281G>T synonymous_variant 0.26
rpoC 764653 c.1284G>C synonymous_variant 0.27
rpoC 764656 c.1287C>T synonymous_variant 0.29
rpoC 764662 c.1293G>C synonymous_variant 0.29
rpoC 764668 c.1299C>A synonymous_variant 0.29
rpoC 764672 p.Gln435Tyr missense_variant 0.26
rpoC 764677 c.1308C>G synonymous_variant 0.28
rpoC 764681 p.Leu438Met missense_variant 0.28
rpoC 764684 p.His439Tyr missense_variant 0.28
rpoC 764695 c.1326T>C synonymous_variant 0.31
rpoC 764701 c.1332C>G synonymous_variant 0.29
rpoC 764705 p.Leu446Glu missense_variant 0.28
rpoC 764716 c.1347G>C synonymous_variant 0.29
rpoC 764737 c.1368G>C synonymous_variant 0.25
rpoC 765462 p.Asn698Ser missense_variant 0.17
rpoC 766840 c.3471C>T synonymous_variant 0.2
rpoC 767032 c.3663G>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777422 c.1059G>T synonymous_variant 0.18
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 1471703 n.-143T>C upstream_gene_variant 0.25
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.43
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.43
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.84
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.9
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.91
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.89
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.89
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.89
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.84
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.81
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.77
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.81
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.77
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.77
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.67
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.5
rrs 1472256 n.411T>G non_coding_transcript_exon_variant 0.5
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.5
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.33
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.33
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.4
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.4
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472508 n.663T>C non_coding_transcript_exon_variant 0.67
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.75
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.75
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.88
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.88
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.78
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.78
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.78
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.78
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.8
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.8
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.89
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.9
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.92
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.88
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.88
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.86
rrs 1472668 n.824dupT non_coding_transcript_exon_variant 0.75
rrs 1472672 n.828_838delTTTCCTTCCTT non_coding_transcript_exon_variant 0.67
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.67
rrs 1472690 n.845_846insACCCCTCG non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 1.0
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 1.0
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.67
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.5
rrs 1472954 n.1109T>A non_coding_transcript_exon_variant 0.92
rrs 1472955 n.1110C>A non_coding_transcript_exon_variant 0.92
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.92
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.92
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.86
rrs 1472971 n.1126G>T non_coding_transcript_exon_variant 0.86
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.86
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.86
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.86
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.86
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.86
rrs 1472991 n.1146G>T non_coding_transcript_exon_variant 0.86
rrs 1472992 n.1147A>T non_coding_transcript_exon_variant 0.86
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.78
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.78
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.78
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.78
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.79
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.79
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.69
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.58
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.5
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.38
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.38
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.3
rrs 1473094 n.1249T>A non_coding_transcript_exon_variant 0.3
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.27
rrs 1473101 n.1256C>G non_coding_transcript_exon_variant 0.27
rrs 1473102 n.1257C>A non_coding_transcript_exon_variant 0.27
rrs 1473107 n.1262G>T non_coding_transcript_exon_variant 0.27
rrs 1473108 n.1263G>C non_coding_transcript_exon_variant 0.27
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.3
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.27
rrs 1473115 n.1270G>C non_coding_transcript_exon_variant 0.27
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.25
rrl 1474768 n.1111C>G non_coding_transcript_exon_variant 0.6
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.67
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.67
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.71
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.75
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.62
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.88
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.88
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.88
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.88
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.89
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.82
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.82
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.82
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.8
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.8
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.75
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.75
rrl 1474927 n.1271delC non_coding_transcript_exon_variant 0.6
rrl 1474931 n.1274G>A non_coding_transcript_exon_variant 0.6
rrl 1475750 n.2093A>C non_coding_transcript_exon_variant 1.0
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.67
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.67
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.67
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.33
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.43
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.6
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.82
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.83
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.81
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.83
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.83
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.83
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.83
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.87
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.91
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.87
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.83
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.87
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.9
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.91
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.93
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.93
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.94
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.93
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.93
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.95
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.95
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 0.94
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.88
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.88
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.87
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.86
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.86
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.86
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.83
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.83
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.8
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.8
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.75
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.64
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.43
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 2155546 p.Asp189Val missense_variant 0.15
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 2170066 p.Ala183Thr missense_variant 0.18
PPE35 2170395 p.Ala73Val missense_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
eis 2715125 p.Thr70Ala missense_variant 1.0
ribD 2987169 p.Gln111Lys missense_variant 0.3
Rv2752c 3065988 p.Glu68Asp 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
Rv3083 3448691 p.Gly63Asp missense_variant 0.13
Rv3083 3448768 c.267delC frameshift_variant 0.14
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449061 c.558C>T synonymous_variant 0.12
fprA 3473948 c.-59C>T upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474942 c.936G>A synonymous_variant 0.15
fprA 3475159 p.Asn385Asp missense_variant 0.83
Rv3236c 3612055 c.1062G>A synonymous_variant 0.12
fbiA 3640567 p.Gly9Arg missense_variant 0.2
alr 3841579 c.-159C>A upstream_gene_variant 0.18
ddn 3986699 c.-145C>A upstream_gene_variant 0.2
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240636 c.774G>A synonymous_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240960 c.1098G>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embC 4242981 p.Met1040Thr missense_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 4249753 p.Leu1080Phe missense_variant 0.15
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268002 c.835C>T synonymous_variant 0.17
aftB 4269339 c.-503C>T upstream_gene_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
ethA 4327557 c.-84G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407774 c.429C>T synonymous_variant 0.14