TB-Profiler result

Run: SRR6044769
Summary

Run ID: SRR6044769

Sample name:

Date: 04-04-2023 11:47:10

Number of reads: 681747

Percentage reads mapped: 85.81

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.5 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.33 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.38 kanamycin, capreomycin, aminoglycosides, amikacin
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 6112 p.Met291Ile missense_variant 0.94
gyrB 6124 c.885C>T synonymous_variant 0.93
gyrB 6668 p.Ala477Ser missense_variant 0.12
gyrB 6932 p.Gln565Lys missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.88
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575811 p.Tyr155Cys missense_variant 0.15
ccsA 620283 c.393T>C synonymous_variant 0.14
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.14
rpoB 762340 p.Arg845Gln missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775966 p.Ala839Ser missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpR5 778226 c.-764T>C upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303038 c.108T>C synonymous_variant 0.11
embR 1416656 p.Val231Glu missense_variant 0.15
embR 1416934 c.414G>A synonymous_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.22
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.45
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.33
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.42
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.5
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.33
rrs 1472160 n.315C>A non_coding_transcript_exon_variant 0.36
rrs 1472161 n.316T>G non_coding_transcript_exon_variant 0.31
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.39
rrs 1472180 n.335A>T non_coding_transcript_exon_variant 0.39
rrs 1472181 n.336G>T non_coding_transcript_exon_variant 0.39
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.29
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.25
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.25
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.4
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.4
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.5
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.4
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.4
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.4
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.5
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.6
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.33
rrs 1472733 n.888G>T non_coding_transcript_exon_variant 0.33
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.33
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.29
rrs 1472742 n.897C>A non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.29
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.25
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.29
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.75
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.5
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.5
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.44
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.38
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.38
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.38
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.29
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.29
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.25
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.27
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.27
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.27
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.27
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.27
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.23
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.23
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.23
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.33
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.42
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.48
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.33
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.33
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.33
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.2
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.22
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.22
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.25
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.25
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.38
rrs 1473346 n.1501G>T non_coding_transcript_exon_variant 0.22
rrs 1473365 n.1520C>A non_coding_transcript_exon_variant 0.22
rrl 1473697 n.40C>T non_coding_transcript_exon_variant 0.29
rrl 1473698 n.41G>A non_coding_transcript_exon_variant 0.29
rrl 1473718 n.61G>T non_coding_transcript_exon_variant 0.33
rrl 1473721 n.64G>A non_coding_transcript_exon_variant 0.4
rrl 1473722 n.65G>T non_coding_transcript_exon_variant 0.4
rrl 1473731 n.74T>A non_coding_transcript_exon_variant 0.33
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 1.0
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 1.0
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 1.0
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 1.0
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 1.0
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 1.0
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 1.0
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 1.0
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 1.0
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 1.0
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 1.0
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 1.0
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 1.0
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 1.0
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 1.0
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 1.0
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 1.0
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 1.0
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 1.0
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 1.0
rrl 1475549 n.1892T>C non_coding_transcript_exon_variant 0.67
rrl 1475639 n.1982C>G non_coding_transcript_exon_variant 0.67
rrl 1475649 n.1992A>G non_coding_transcript_exon_variant 0.67
rrl 1475655 n.1998T>G non_coding_transcript_exon_variant 0.67
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.67
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.67
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.6
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.6
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.75
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.71
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.62
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.62
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.62
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.62
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.62
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.62
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.62
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.62
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.62
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.5
rrl 1475772 n.2115A>C non_coding_transcript_exon_variant 0.2
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.5
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.2
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.87
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.87
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.87
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.87
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.87
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.87
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.83
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.83
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.83
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.8
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.5
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.5
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.5
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.5
rrl 1476110 n.2453G>T non_coding_transcript_exon_variant 0.33
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.44
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.44
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.44
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.5
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.44
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.38
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.38
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.33
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.4
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.5
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.4
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.4
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.5
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.5
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.5
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.67
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.67
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.25
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.22
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.2
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.2
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.43
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.13
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.29
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.25
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.32
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.22
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.62
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.44
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.46
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.46
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.46
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.5
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.5
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.5
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.57
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.31
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.18
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.18
rrl 1476586 n.2929C>T non_coding_transcript_exon_variant 0.18
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.17
rrl 1476603 n.2946G>T non_coding_transcript_exon_variant 0.17
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.15
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.15
rrl 1476613 n.2956G>A non_coding_transcript_exon_variant 0.15
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.15
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.18
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.14
rrl 1476628 n.2971T>G non_coding_transcript_exon_variant 0.14
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.14
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.14
inhA 1674599 p.Ala133Val missense_variant 0.12
inhA 1674646 c.446_447delTC frameshift_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102095 c.948C>T synonymous_variant 1.0
katG 2154055 p.Lys686Arg missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168444 c.2169G>A synonymous_variant 0.31
PPE35 2169488 c.1125G>C synonymous_variant 0.11
PPE35 2169491 c.1122T>C synonymous_variant 0.11
PPE35 2169587 c.1026G>A synonymous_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289396 c.-155T>A upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519024 p.Asp304Asn missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726250 p.Gly20Ser missense_variant 0.13
ahpC 2726338 p.Val49Gly missense_variant 0.31
ribD 2987035 p.Gly66Asp missense_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087152 c.333C>T synonymous_variant 0.17
fbiD 3339327 c.210T>A synonymous_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448805 p.Gly101Asp missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.18
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640468 c.-75G>C upstream_gene_variant 1.0
fbiA 3641444 p.Val301Ala missense_variant 0.11
clpC1 4039610 c.1095G>C synonymous_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044254 p.Ile10Phe missense_variant 0.11
embC 4240334 p.Thr158Ala missense_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244167 p.Ala312Val missense_variant 1.0
embA 4245378 p.Tyr716His missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.15
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4246614 p.Gly34Glu missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268695 p.Val48Ile missense_variant 0.14
aftB 4268755 p.Ala28Thr missense_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326432 p.Leu348Phe missense_variant 1.0
whiB6 4338243 c.279C>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407988 p.Ala72Val missense_variant 1.0