Kartchner 16S Sequence QA and Trimming

Trim Steps:

  1. Minimum avg. quality score: 30
  2. No N's
  3. Minimum length: 95
  4. Maximum length: 120
  5. Forward primer sequence: [AC][AT]ACGCGA[AG]GAACCTTACC
  6. Reverse primer sequence: ATGG[CT]TGTCGTCAGC
  7. Trim length: 75 (after removal of forward primer)

    Note, sequences provided by AGI were already filtered for correct barcode. 552,944 total reads were generated, of which 551,526 (99.7%) had correct barcode and were transmitted for analysis.

    Results

    Sample # Reads Avg qual >= 30 no N's >=95 <=120 Forward Primer Reverse Primer Pass
    A 34360 30453 (88%) 29237 (85%) 29213 (85%) 29119 (84%) 27964 (81%) 27106 (78%) 27106 (78%)
    B 32021 27793 (86%) 27044 (84%) 26995 (84%) 26672 (83%) 24789 (77%) 23979 (74%) 23979 (74%)
    BL 49712 45636 (91%) 44139 (88%) 44107 (88%) 44103 (88%) 41920 (84%) 40579 (81%) 40579 (81%)
    C 52307 47559 (90%) 46778 (89%) 46742 (89%) 46708 (89%) 44529 (85%) 43131 (82%) 43131 (82%)
    CA 38690 33271 (85%) 32241 (83%) 32079 (82%) 31845 (82%) 30551 (78%) 29174 (75%) 29174 (75%)
    D 44771 40262 (89%) 39680 (88%) 39654 (88%) 39256 (87%) 37904 (84%) 36329 (81%) 36329 (81%)
    E 42610 37796 (88%) 37216 (87%) 37177 (87%) 37091 (87%) 35894 (84%) 34896 (81%) 34896 (81%)
    F 45674 41614 (91%) 39183 (85%) 39140 (85%) 38799 (84%) 37254 (81%) 35625 (77%) 35625 (77%)
    OR 46029 39916 (86%) 38356 (83%) 38247 (83%) 38188 (82%) 36426 (79%) 34719 (75%) 34719 (75%)
    RO 50826 44890 (88%) 43365 (85%) 43284 (85%) 43254 (85%) 40867 (80%) 38919 (76%) 38919 (76%)
    ST 56785 49338 (86%) 48738 (85%) 48346 (85%) 48208 (84%) 46717 (82%) 44721 (78%) 44721 (78%)
    W 57741 53361 (92%) 51652 (89%) 51604 (89%) 51501 (89%) 49280 (85%) 47487 (82%) 47487 (82%)
    TOTAL 551526 491889 (89%) 477629 (86%) 476588 (86%) 474744 (86%) 454095 (82%) 436665 (79%) 436665 (79%)

    Length Stats

    Avg length of input sequences: 103.1
    Std deviation: 4.6
    Min length 40, max length 232

    Lengths of unfiltered reads

    length# of sequences
    401
    414
    4218
    43323
    4436
    4568
    4641
    4710
    485
    499
    508
    519
    525
    533
    542
    553
    563
    579
    5812
    597
    6022
    617
    6215
    6313
    6418
    652
    6619
    6719
    6837
    69158
    7031
    718
    7216
    7319
    7414
    7511
    768
    772
    793
    802
    814
    823
    835
    843
    851
    862
    873
    8910
    9014
    9116
    9210
    9321
    9421
    9560
    96138
    97979
    983554
    9910256
    10093058
    10150370
    10256565
    10368308
    10461946
    10574705
    10616286
    10726393
    10811459
    1093006
    1101833
    1111043
    112173
    113124
    114173
    115505
    1165712
    1171858
    118311
    11969
    12027
    12151
    12240
    123123
    1241196
    125148
    12621
    1275
    1284
    1293
    1301
    1313
    1323
    1334
    1347
    1354
    1361
    1372
    1381
    1401
    1421
    1551
    1591
    1611
    1631
    1781
    1832
    1861
    1872
    1881
    1891
    1912
    1925
    1932
    1941
    1951
    1962
    1971
    1982
    2111
    2123
    2136
    21420
    21544
    21649
    21761
    21829
    2191
    2201
    2291
    2322