TCW overview for mus

Project: mus
 
INPUT
   Counts: 
      SEQID  ID            SIZE  TITLE                 #REPS  
      ENS72  B6Br    32,485,203  B6 Brain                  4  
      ENS72  B6Kid   36,556,756  B6 Kidney                 4  
      ENS72  B6Liv   50,824,622  B6 Liver                  4  
      ENS72  B6Mus   63,564,680  B6 Muscle                 4  
      ENS72  BcBr    36,537,801  Bc Brain                  4  
      ENS72  BcKid   36,387,081  Bc Kidney                 4  
      ENS72  BcLiv   23,670,157  Bc Liver                  4  
      ENS72  BcMus   36,169,665  Bc Muscle                 4  
      ENS72  NYfBr   15,573,243  Young F1 Brain (1)        4  
      ENS72  NYfKid  11,600,990  Young F1 Kidney  (1)      4  
      ENS72  NYfLiv  19,591,723  Young F1 Liver (1)        4  
      ENS72  NYfMus  22,394,572  Young F1 Muscle (1)       4  
      ENS72  OfBr    39,532,281  Old F1 Brain              4  
      ENS72  OfKid   39,571,340  Old F1 Kidney             4  
      ENS72  OfLiv   49,793,540  Old F1 Liver              4  
      ENS72  OfMus   70,986,198  Old F1 Muscle             4  
      ENS72  YfBr    21,211,369  Young F1 Brain (2)        4  
      ENS72  YfKid   37,006,917  Young F1 Kidney (2)       4  
      ENS72  YfLiv   43,411,024  Young F1 Liver (2)        4  
      ENS72  YfMus   24,424,911  Young F1 Muscle (2)       4  

   Sequences: 
      SEQID    SIZE  TITLE                      STRAIN    AVG-len  MED-len  
      ENS72  47,226  Mouse (GRCm38p2) proteins  C57BL/6J      454      314  

ANNOTATION
   Annotated with TCW release: 1.6.7
   Annotation date: 01-Dec-16
   AnnoDB Statistics:
      Sequences with hits:           35,884  (76.0%)                                   
      Sequence coverage by hits:      72.0%  (Bases: 21,450,335; covered: 15,450,817)  
      Total Sequence hits:          824,476                                            
      Unique hits:                  228,487                                            
      Unique hits with GOs:         169,787  (74.3%)                                   
      Sequences with GOs:            33,621  (71.2%)                                   
      Sequences best hit with GOs:   29,873  (63.3%)                                   
      Unique GOs                     21,100                                            
      Slims from goslim_generic         144                                            

   Annotation databases: 2   (see Legend at end)
      TYPE   TAXO     UNIQUE    ONLY    EVAL    ANNO    TOTAL  SIM>=40  SIM<40  
      sp    rodents   25,671     925  14,912  15,878  221,781    49.7%   50.3%  
      tr    rodents  202,816  14,554  20,972  20,006  602,695    88.0%   12.0%  

   Top 15 species from total: 500
      SPECIES (25 char)            EVAL    ANNO  TOTAL     SPECIES                 EVAL   ANNO  TOTAL  
      Mus musculus               27,839  27,810   334k     Mesocricetus auratus      28     39     2k  
      Rattus norvegicus           3,148   3,691   141k     Mus spicilegus            12     12    299  
      Cricetulus griseus          1,356   1,718    71k     Mus spretus               11     12    301  
      Heterocephalus glaber         833   1,169    66k     Meriones unguiculatus      9     11    493  
      Neotoma lepida                832      95    40k     Castor fiber               9     10    603  
      Ictidomys tridecemlineatu     649     174    55k     Microtus ochrogaster       8      9    284  
      Fukomys damarensis            620     864    46k     Rattus sp.                 8      7    215  
      Cavia porcellus               443     167    54k     Other                     79     96     7k  

EXPRESSION
   RPKM: 
                      0-1         2-4        5-10       11-50      51-100      101-1k     1k-5k       >5k  
      B6Br    18,729(40%)  3,278 (7%)  3,520 (7%)  8,333(18%)  3,096 (7%)  5,017(11%)  604 (1%)   74(<1%)  
      B6Kid   21,615(46%)  3,206 (7%)  3,444 (7%)  7,019(15%)  2,535 (5%)  4,087 (9%)  639 (1%)  118(<1%)  
      B6Liv   26,027(55%)  2,871 (6%)  2,938 (6%)  5,757(12%)  1,838 (4%)  3,154 (7%)  516 (1%)  103(<1%)  
      B6Mus   25,493(54%)  2,947 (6%)  3,052 (6%)  5,919(13%)  1,910 (4%)  3,052 (6%)  448 (1%)  102(<1%)  
      BcBr    18,646(39%)  3,223 (7%)  3,535 (7%)  8,387(18%)  3,155 (7%)  5,085(11%)  614 (1%)   67(<1%)  
      BcKid   22,005(47%)  3,220 (7%)  3,415 (7%)  6,771(14%)  2,378 (5%)  4,031 (9%)  631 (1%)  133(<1%)  
      BcLiv   26,699(57%)  2,787 (6%)  2,863 (6%)  5,613(12%)  1,766 (4%)  2,981 (6%)  444 (1%)  100(<1%)  
      BcMus   24,591(52%)  3,037 (6%)  3,268 (7%)  6,402(14%)  1,945 (4%)  3,043 (6%)  426 (1%)   97(<1%)  
      NYfBr   19,142(41%)  3,121 (7%)  3,545 (8%)  8,322(18%)  3,128 (7%)  5,003(11%)  587 (1%)   67(<1%)  
      NYfKid  21,850(46%)  3,058 (6%)  3,452 (7%)  7,147(15%)  2,511 (5%)  4,164 (9%)  617 (1%)  100(<1%)  
      NYfLiv  25,924(55%)  2,856 (6%)  2,997 (6%)  5,824(12%)  1,845 (4%)  3,000 (6%)  442 (1%)  105(<1%)  
      NYfMus  24,215(51%)  3,263 (7%)  3,380 (7%)  6,298(13%)  1,890 (4%)  3,007 (6%)  421 (1%)   93(<1%)  
      OfBr    19,018(40%)  3,214 (7%)  3,514 (7%)  8,138(17%)  3,129 (7%)  5,016(11%)  632 (1%)   64(<1%)  
      OfKid   22,296(47%)  3,091 (7%)  3,342 (7%)  6,778(14%)  2,359 (5%)  4,013 (8%)  666 (1%)  132(<1%)  
      OfLiv   26,114(55%)  2,859 (6%)  2,961 (6%)  5,555(12%)  1,851 (4%)  3,079 (7%)  502 (1%)  110(<1%)  
      OfMus   24,939(53%)  2,881 (6%)  3,087 (7%)  6,041(13%)  2,019 (4%)  3,253 (7%)  491 (1%)  104(<1%)  
      YfBr    19,269(41%)  3,118 (7%)  3,624 (8%)  8,158(17%)  3,026 (6%)  4,902(10%)  593 (1%)   78(<1%)  
      YfKid   22,711(48%)  3,153 (7%)  3,208 (7%)  6,626(14%)  2,354 (5%)  4,001 (8%)  657 (1%)  129(<1%)  
      YfLiv   26,484(56%)  2,839 (6%)  2,957 (6%)  5,415(11%)  1,809 (4%)  3,004 (6%)  503 (1%)  112(<1%)  
      YfMus   26,135(55%)  2,915 (6%)  3,114 (7%)  5,796(12%)  1,785 (4%)  2,797 (6%)  380 (1%)   93(<1%)  

   Sequence DE:
                   <1e-5     <1e-4      <0.001       <0.01       <0.05  
      BcNYfBr    77(<1%)  108(<1%)    175(<1%)    312 (1%)    537 (1%)  
      BcNYfKid  227(<1%)  366 (1%)    615 (1%)  1,215 (3%)  2,188 (5%)  
      BcNYfLiv  187(<1%)  268 (1%)    480 (1%)    907 (2%)  1,674 (4%)  
      BcNYfMus  360 (1%)  541 (1%)    975 (2%)  2,104 (4%)  3,974 (8%)  
      BcOfBr      7(<1%)   13(<1%)     27(<1%)     48(<1%)     86(<1%)  
      BcOfKid    24(<1%)   31(<1%)     38(<1%)     73(<1%)    110(<1%)  
      BcOfLiv    95(<1%)  126(<1%)    198(<1%)    355 (1%)    627 (1%)  
      BcOfMus   230(<1%)  361 (1%)    649 (1%)  1,432 (3%)  2,979 (6%)  
      B6NYfBr    35(<1%)   45(<1%)     79(<1%)    185(<1%)    399 (1%)  
      B6NYfKid  124(<1%)  187(<1%)    308 (1%)    613 (1%)  1,159 (2%)  
      B6NYfLiv  107(<1%)  161(<1%)    292 (1%)    600 (1%)  1,213 (3%)  
      B6NYfMus  453 (1%)  644 (1%)  1,065 (2%)  2,032 (4%)  3,541 (7%)  
      B6OfBr      3(<1%)    3(<1%)      5(<1%)     14(<1%)     44(<1%)  
      B6OfKid    12(<1%)   16(<1%)     24(<1%)     48(<1%)     75(<1%)  
      B6OfLiv    50(<1%)   68(<1%)     93(<1%)    180(<1%)    325 (1%)  
      B6OfMus    73(<1%)  100(<1%)    158(<1%)    299 (1%)    550 (1%)  

   Gene Ontology DE:
                   <1e-5     <1e-4    <0.001       <0.01       <0.05  
      BcNYfBr   169 (1%)  254 (1%)  417 (2%)    804 (4%)  1,614 (8%)  
      BcNYfKid  247 (1%)  353 (2%)  505 (2%)    957 (5%)  1,936 (9%)  
      BcNYfLiv   92(<1%)  151 (1%)  285 (1%)    672 (3%)  1,635 (8%)  
      BcNYfMus  155 (1%)  284 (1%)  583 (3%)  1,320 (6%)  2,643(13%)  
      BcOfBr     13(<1%)   44(<1%)   93(<1%)    328 (2%)    878 (4%)  
      BcOfKid    21(<1%)   34(<1%)   84(<1%)    290 (1%)    736 (3%)  
      BcOfLiv    64(<1%)  100(<1%)  190 (1%)    475 (2%)  1,189 (6%)  
      BcOfMus   347 (2%)  545 (3%)  916 (4%)  1,873 (9%)  3,443(16%)  
      B6NYfBr    39(<1%)   62(<1%)  135 (1%)    357 (2%)    900 (4%)  
      B6NYfKid   89(<1%)  137 (1%)  256 (1%)    587 (3%)  1,418 (7%)  
      B6NYfLiv   59(<1%)   91(<1%)  220 (1%)    505 (2%)  1,110 (5%)  
      B6NYfMus  146 (1%)  216 (1%)  383 (2%)    824 (4%)  1,562 (7%)  
      B6OfBr      0 (0%)    0 (0%)    3(<1%)     44(<1%)    202 (1%)  
      B6OfKid     0 (0%)    1(<1%)    8(<1%)    122 (1%)    410 (2%)  
      B6OfLiv    90(<1%)  135 (1%)  246 (1%)    536 (3%)  1,207 (6%)  
      B6OfMus    25(<1%)   70(<1%)  143 (1%)    517 (2%)  1,394 (7%)  

SEQUENCES
   Build date: 01-Dec-16
   Proteins loaded from external source

   Protein lengths:
           1-100      101-500    501-1000  1001-2000  2001-3000  3001-4000  4001-5000    >5000  
      5,397(11%)  27,755(59%)  9,931(21%)  3,423(7%)    494(1%)   106(<1%)    77(<1%)  43(<1%)  


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PROCESSING INFORMATION:
   AnnoDB Files:
      Type  Taxo     FILE                          DB DATE    ADD DATE   EXECUTE                                    
      sp    rodents  uniprot_sprot_rodents.fasta   21-Oct-16  01-Dec-16  blast  -evalue 1e-10 -max_target_seqs 25   
      tr    rodents  uniprot_trembl_rodents.fasta  21-Oct-16  01-Dec-16  diamond  -e 1e-03 -k 25                    

   Gene Ontology: go_201610-termdb-tables.tar.gz    [GOs added with sTCW v1.6.7 (29-Nov-16)]
   GO Slim: goslim_generic

   DE (Differential Expression) computation: 
      DE column    Conditions                     Method
      BcNYfBr      BcBr : NYfBr                   edgeR
      BcNYfKid     BcKid : NYfKid                 edgeR
      BcNYfLiv     BcLiv : NYfLiv                 edgeR
      BcNYfMus     BcMus : NYfMus                 edgeR
      BcOfBr       BcBr : OfBr                    edgeR
      BcOfKid      BcKid : OfKid                  edgeR
      BcOfLiv      BcLiv : OfLiv                  edgeR
      BcOfMus      BcMus : OfMus                  edgeR
      B6NYfBr      B6Br : NYfBr                   edgeR
      B6NYfKid     B6Kid : NYfKid                 edgeR
      B6NYfLiv     B6Liv : NYfLiv                 edgeR
      B6NYfMus     B6Mus : NYfMus                 edgeR
      B6OfBr       B6Br : OfBr                    edgeR
      B6OfKid      B6Kid : OfKid                  edgeR
      B6OfLiv      B6Liv : OfLiv                  edgeR
      B6OfMus      B6Mus : OfMus                  edgeR

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LEGEND:
   annoDB:
      Unique  #unique hits to this annoDB, i.e. unique annoDB identifiers
      ONLY    #TCW sequences that hit this annoDB and no others
      EVAL    #TCW sequences with the best eval from this annoDB
      ANNO    #TCW sequences with the best annotation from this annoDB 
      TOTAL   #Total sequence-hits pairs to this annoDB
      SIM>=40 #TCW sequences with >=40 blast %similarity to hit
      SIM< 40 #TCW sequences with <40 blast %similarity to hit

   Species:
      SPECIES If the species name is >25 characters, it is truncated to 25
      EVAL    #TCW sequences with the best eval from this species
      ANNO    #TCW sequences with the best annotation from this species 
      Total   #Total hits to this species

   ANNO details:
      Descriptions may not contain words such as 'uncharacterized', 'hypothetical_protein', 'orf', etc
      Precedence is given to SwissProt hits since they are manually curated