TB-Profiler result

Run: SRR21469202
Summary

Run ID: SRR21469202

Sample name:

Date: 04-04-2023 02:06:31

Number of reads: 1376284

Percentage reads mapped: 79.24

Strain: La1.7.1

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
La1.7 M.bovis None None 1.0
La1.7.1 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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.21 kanamycin, capreomycin, aminoglycosides, amikacin
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 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
ccsA 619706 c.-185G>A upstream_gene_variant 1.0
rpoB 762879 p.Met1025Leu missense_variant 0.11
rpoC 762899 c.-471G>C upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763589 p.Ile74Val missense_variant 0.13
rpoC 763609 c.240C>G synonymous_variant 0.13
rpoC 763614 c.246_251delGACCCG disruptive_inframe_deletion 0.14
rpoC 763622 p.Ala85Thr missense_variant 0.13
rpoC 763627 c.258_259insAGCTCC conservative_inframe_insertion 0.14
rpoC 763630 c.261G>C synonymous_variant 0.14
rpoC 763642 c.273G>C synonymous_variant 0.16
rpoC 763648 c.279C>T synonymous_variant 0.17
rpoC 763660 c.291T>C synonymous_variant 0.16
rpoC 763666 c.297G>T synonymous_variant 0.16
rpoC 763696 c.327T>C synonymous_variant 0.12
rpoC 763708 c.339G>C synonymous_variant 0.11
rpoC 763714 c.345G>C synonymous_variant 0.11
rpoC 764446 c.1077T>C synonymous_variant 0.11
rpoC 764449 c.1080G>C synonymous_variant 0.11
rpoC 764455 c.1086G>C synonymous_variant 0.11
rpoC 764458 c.1089G>C synonymous_variant 0.11
rpoC 764461 c.1092A>G synonymous_variant 0.11
rpoC 764485 c.1116G>C synonymous_variant 0.16
rpoC 764497 c.1128A>G synonymous_variant 0.17
rpoC 764498 p.Ser377Ala missense_variant 0.17
rpoC 764509 c.1140G>A synonymous_variant 0.17
rpoC 764521 c.1152T>C synonymous_variant 0.18
rpoC 764524 c.1155C>T synonymous_variant 0.16
rpoC 764530 c.1161C>T synonymous_variant 0.15
rpoC 764533 c.1164C>T synonymous_variant 0.16
rpoC 764536 c.1167G>C synonymous_variant 0.16
rpoC 764548 c.1179G>T synonymous_variant 0.15
rpoC 764549 p.Pro394Thr missense_variant 0.15
rpoC 764561 p.Pro398Ala missense_variant 0.14
rpoC 764566 c.1197C>G synonymous_variant 0.15
rpoC 764575 c.1206T>C synonymous_variant 0.12
rpoC 764576 c.1207_1208delTCinsAG synonymous_variant 0.12
rpoC 764581 c.1212T>C synonymous_variant 0.13
rpoC 764582 p.Leu405Met missense_variant 0.12
rpoC 764587 c.1218C>G synonymous_variant 0.12
rpoC 764593 c.1224C>T synonymous_variant 0.14
rpoC 764602 c.1233C>T synonymous_variant 0.13
rpoC 764605 c.1236G>T synonymous_variant 0.13
rpoC 764611 c.1242G>T synonymous_variant 0.14
rpoC 764626 c.1257C>A synonymous_variant 0.13
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
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.3
Rv1258c 1406161 p.Ala394Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.14
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.14
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.14
rrs 1472507 n.662C>T non_coding_transcript_exon_variant 0.22
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.26
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.23
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.23
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.26
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.23
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.23
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 0.22
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.21
rrs 1472660 n.815T>A non_coding_transcript_exon_variant 0.19
rrs 1472666 n.821G>T non_coding_transcript_exon_variant 0.2
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.21
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.21
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.21
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.19
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.19
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.18
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.18
rrs 1472694 n.849C>A non_coding_transcript_exon_variant 0.18
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.18
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.2
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.15
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.12
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.19
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.18
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.19
rrs 1472993 n.1148G>T non_coding_transcript_exon_variant 0.18
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.19
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.26
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.26
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.27
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.34
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.35
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.35
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.35
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.32
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.32
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.32
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.32
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.32
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.3
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.3
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.28
rrs 1473269 n.1424C>T non_coding_transcript_exon_variant 0.19
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.2
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.14
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.14
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.23
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 0.22
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.21
rrl 1474202 n.545T>A non_coding_transcript_exon_variant 0.21
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.26
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.21
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.15
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.15
rrl 1474275 n.618T>A non_coding_transcript_exon_variant 0.15
rrl 1474280 n.623C>T non_coding_transcript_exon_variant 0.13
rrl 1474281 n.624A>G non_coding_transcript_exon_variant 0.15
rrl 1474291 n.635_645delTTCCTCTCCGG non_coding_transcript_exon_variant 0.14
rrl 1474305 n.648G>T non_coding_transcript_exon_variant 0.12
rrl 1474308 n.653_654delTG non_coding_transcript_exon_variant 0.12
rrl 1474316 n.659T>C non_coding_transcript_exon_variant 0.12
rrl 1474317 n.660G>A non_coding_transcript_exon_variant 0.12
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.12
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.14
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.13
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.13
rrl 1474466 n.809G>A non_coding_transcript_exon_variant 0.11
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.14
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.14
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.16
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.16
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.16
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.16
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.16
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.16
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.14
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.13
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.1
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.12
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.12
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.12
rrl 1474723 n.1066G>A non_coding_transcript_exon_variant 0.12
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.12
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.13
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.12
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.12
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.12
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1474770 n.1113G>A non_coding_transcript_exon_variant 0.13
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.12
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.13
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.13
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.13
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.14
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.14
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.14
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.14
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.1
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.2
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.2
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.19
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.26
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.27
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.27
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.28
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.28
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.37
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.39
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.38
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.34
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.3
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.3
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.34
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.32
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.32
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.33
rrl 1476025 n.2368G>T non_coding_transcript_exon_variant 0.29
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.29
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.29
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.29
rrl 1476040 n.2383C>T non_coding_transcript_exon_variant 0.29
rrl 1476045 n.2388G>C non_coding_transcript_exon_variant 0.29
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.29
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.29
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.27
rrl 1476076 n.2419A>G non_coding_transcript_exon_variant 0.3
rrl 1476079 n.2422G>A non_coding_transcript_exon_variant 0.28
rrl 1476080 n.2423T>C non_coding_transcript_exon_variant 0.3
rrl 1476081 n.2424A>T non_coding_transcript_exon_variant 0.3
rrl 1476082 n.2425T>C non_coding_transcript_exon_variant 0.29
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.28
rrl 1476087 n.2430C>T non_coding_transcript_exon_variant 0.28
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.27
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.28
rrl 1476104 n.2448delG non_coding_transcript_exon_variant 0.27
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.26
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.3
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.36
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.31
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.33
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.37
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.37
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.35
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.35
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.39
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.4
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.39
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.39
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.41
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.38
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.38
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.38
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.38
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.38
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.38
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.38
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.38
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.43
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.47
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.46
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.41
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.23
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.23
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.23
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.23
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.24
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.24
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.22
rrl 1476544 n.2887T>A non_coding_transcript_exon_variant 0.23
rrl 1476566 n.2909A>T non_coding_transcript_exon_variant 0.19
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.18
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.1
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103092 c.-50T>C upstream_gene_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
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 0.93
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
fbiB 3642478 p.Asp315Ala missense_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 0.99
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 0.98
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267100 c.1737C>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
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0