TB-Profiler result

Run: SRR5341365
Summary

Run ID: SRR5341365

Sample name:

Date: 04-04-2023 10:17:24

Number of reads: 1788344

Percentage reads mapped: 77.36

Strain: lineage3

Drug-resistance: Pre-XDR-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
lineage3 East-African-Indian CAS RD750 0.99
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.19 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.35 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.27 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.98 ethambutol
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.9
rpoB 761990 c.2184G>C synonymous_variant 0.12
rpoB 762003 p.Asn733Gln missense_variant 0.12
rpoB 762016 p.Glu737Ala missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762896 c.-474G>C upstream_gene_variant 0.12
rpoC 762917 c.-453C>G upstream_gene_variant 0.16
rpoC 762929 c.-441G>C upstream_gene_variant 0.15
rpoC 762959 c.-411G>C upstream_gene_variant 0.11
rpoC 762965 c.-405T>A upstream_gene_variant 0.12
rpoC 762971 c.-399G>C upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763546 c.177A>G synonymous_variant 0.11
rpoC 763550 p.Tyr61Asp missense_variant 0.11
rpoC 763589 p.Ile74Val missense_variant 0.21
rpoC 763622 p.Ala85Ser missense_variant 0.16
rpoC 763633 c.264T>C synonymous_variant 0.17
rpoC 763636 c.267T>C synonymous_variant 0.15
rpoC 763639 p.Glu90Asp missense_variant 0.15
rpoC 763642 c.273G>C synonymous_variant 0.17
rpoC 763660 c.291T>C synonymous_variant 0.17
rpoC 763666 c.297G>C synonymous_variant 0.18
rpoC 763672 c.303C>G synonymous_variant 0.15
rpoC 763693 c.324G>A synonymous_variant 0.18
rpoC 763696 c.327T>C synonymous_variant 0.18
rpoC 763708 c.339G>C synonymous_variant 0.18
rpoC 763714 c.345G>C synonymous_variant 0.15
rpoC 763717 c.348T>C synonymous_variant 0.17
rpoC 763744 c.375G>C synonymous_variant 0.13
rpoC 763751 p.Ile128Val missense_variant 0.12
rpoC 764353 c.984G>C synonymous_variant 0.17
rpoC 764359 c.990C>G synonymous_variant 0.17
rpoC 764371 c.1002G>C synonymous_variant 0.19
rpoC 764377 c.1008C>G synonymous_variant 0.18
rpoC 764380 c.1011G>C synonymous_variant 0.18
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.19
rpoC 764398 c.1029G>C synonymous_variant 0.19
rpoC 764404 c.1035C>T synonymous_variant 0.12
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.12
rpoC 764470 c.1101C>G synonymous_variant 0.1
rpoC 764509 c.1140G>C synonymous_variant 0.13
rpoC 764521 c.1152T>C synonymous_variant 0.19
rpoC 764527 c.1158C>T synonymous_variant 0.22
rpoC 764536 c.1167G>C synonymous_variant 0.21
rpoC 764539 c.1170C>G synonymous_variant 0.22
rpoC 764548 c.1179G>C synonymous_variant 0.3
rpoC 764560 c.1191T>C synonymous_variant 0.28
rpoC 764566 c.1197C>G synonymous_variant 0.3
rpoC 764575 c.1206T>C synonymous_variant 0.3
rpoC 764581 c.1212T>C synonymous_variant 0.32
rpoC 764582 p.Leu405Met missense_variant 0.31
rpoC 764605 c.1236G>C synonymous_variant 0.39
rpoC 764611 c.1242G>C synonymous_variant 0.37
rpoC 764632 c.1263T>C synonymous_variant 0.36
rpoC 764650 c.1281G>T synonymous_variant 0.35
rpoC 764677 c.1308C>G synonymous_variant 0.32
rpoC 764695 c.1326T>C synonymous_variant 0.27
rpoC 764701 c.1332C>G synonymous_variant 0.23
rpoC 764706 p.Leu446Gln missense_variant 0.22
rpoC 764713 c.1344G>A synonymous_variant 0.2
rpoC 764746 c.1377G>C synonymous_variant 0.18
rpoC 764749 c.1380G>C synonymous_variant 0.18
rpoC 764758 c.1389C>G synonymous_variant 0.16
rpoC 764764 c.1395T>C synonymous_variant 0.14
rpoC 764781 p.Ser471Thr missense_variant 0.1
rpoC 766485 p.Val1039Gly missense_variant 0.33
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472086 n.241T>C non_coding_transcript_exon_variant 0.14
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.19
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.2
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.2
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.18
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.18
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.37
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.36
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.27
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.14
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.11
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.19
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.2
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.22
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.38
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.44
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.43
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.32
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.18
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.17
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.17
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.21
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.16
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.36
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.35
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.42
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.43
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.36
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.35
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.37
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.26
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.26
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.26
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.27
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.27
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.24
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.23
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.23
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.21
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.22
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.22
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.21
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.22
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.24
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.23
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.26
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.36
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.35
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.31
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.32
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.28
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.28
rrl 1474155 n.498G>A non_coding_transcript_exon_variant 0.18
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.21
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.2
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.2
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.2
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.2
rrl 1474186 n.529A>T non_coding_transcript_exon_variant 0.2
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.19
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.18
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.18
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.27
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.28
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.32
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.33
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.29
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.29
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.29
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.31
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.3
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.25
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.24
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.26
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.26
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.26
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.26
rrl 1474662 n.1005C>A non_coding_transcript_exon_variant 0.33
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.31
rrl 1474688 n.1031G>T non_coding_transcript_exon_variant 0.28
rrl 1474710 n.1053T>G non_coding_transcript_exon_variant 0.26
rrl 1474711 n.1054_1055insTAA non_coding_transcript_exon_variant 0.25
rrl 1474714 n.1058delT non_coding_transcript_exon_variant 0.25
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.26
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.31
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.32
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.26
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.26
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.27
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.33
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.33
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.33
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.35
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.4
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.39
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.37
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.36
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.36
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.15
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.14
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.12
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.12
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 0.12
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.13
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.13
rrl 1475549 n.1892T>C non_coding_transcript_exon_variant 0.1
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.26
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 0.28
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.27
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.27
rrl 1475766 n.2109G>C non_coding_transcript_exon_variant 0.26
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.31
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.47
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.42
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.41
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.39
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.42
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.44
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.45
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.42
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.36
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.34
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.34
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.3
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.26
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.25
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.23
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.23
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.2
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.1
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.11
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.27
rrl 1476164 n.2507A>T non_coding_transcript_exon_variant 0.27
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.26
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.32
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.3
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.3
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.31
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.31
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.29
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.29
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.21
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.15
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.12
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.14
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.11
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.24
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.13
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.35
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.37
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.13
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.39
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.34
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.41
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.26
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.27
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.2
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 0.23
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.19
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.2
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.24
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.17
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.19
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.16
rrl 1476586 n.2929C>T non_coding_transcript_exon_variant 0.16
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.16
rrl 1476603 n.2946G>T non_coding_transcript_exon_variant 0.14
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.14
rpsA 1833661 c.120A>G synonymous_variant 0.12
rpsA 1833668 p.Ile43Val missense_variant 0.14
rpsA 1833676 c.135A>G synonymous_variant 0.15
rpsA 1833679 c.138G>C synonymous_variant 0.16
rpsA 1833685 c.144G>C synonymous_variant 0.18
rpsA 1833694 c.153G>C synonymous_variant 0.18
rpsA 1833697 c.156C>G synonymous_variant 0.2
rpsA 1833709 c.168C>G synonymous_variant 0.22
rpsA 1833721 c.180A>G synonymous_variant 0.22
rpsA 1833727 c.186G>C synonymous_variant 0.2
rpsA 1833733 c.192C>G synonymous_variant 0.14
rpsA 1833734 p.Ala65Ser missense_variant 0.14
rpsA 1833742 c.201A>G synonymous_variant 0.17
rpsA 1834000 c.459G>C synonymous_variant 0.12
rpsA 1834015 c.474G>C synonymous_variant 0.1
rpsA 1834040 p.Lys167Gln missense_variant 0.11
rpsA 1834043 p.Glu168Lys missense_variant 0.11
rpsA 1834046 p.Ile169Leu missense_variant 0.13
rpsA 1834231 c.690T>C synonymous_variant 0.1
rpsA 1834240 c.699T>G synonymous_variant 0.1
rpsA 1834243 c.702G>C synonymous_variant 0.1
rpsA 1834249 c.708T>C synonymous_variant 0.13
rpsA 1834261 c.720A>G synonymous_variant 0.16
rpsA 1834264 c.723G>C synonymous_variant 0.16
rpsA 1834294 c.753G>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
folC 2747480 p.Glu40Ala missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 1.0
rpoA 3878417 p.Gly31Ser missense_variant 0.61
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0