/usr/local/genome/bin/phrap test_project.fasta.screen -new_ace -view
phrap version 0.990329
Run date:time 010621:164002
Query file(s): test_project.fasta.screen
Presumed sequence type: DNA
Pairwise comparison algorithm: banded Smith-Waterman
Score matrix (set by value of penalty: -2)
A C G T N X
A 1 -2 -2 -2 0 -3
C -2 1 -2 -2 0 -3
G -2 -2 1 -2 0 -3
T -2 -2 -2 1 0 -3
N 0 0 0 0 0 0
X -3 -3 -3 -3 0 -3
Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3,
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 14, maxmatch: 30, max_group_size: 20, minscore: 30, bandwidth: 14, indexwordsize: 10
vector_bound: 80
word_raw: 0
trim_penalty: -2, trim_score: 20, trim_qual: 13, maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8, confirm_trim: 1, confirm_penalty: -5, confirm_score: 30
node_seg: 8, node_space: 4
forcelevel: 0, bypasslevel: 1
max_subclone_size: 5000
Sequence file: test_project.fasta.screen 4 entries
Residue counts:
A 799
C 688
G 670
N 1
T 732
X 99
Total 2989
Read name analysis:
# Reads # templates
1 4
Suffix counts:
(no suffix) 4
Templates inferred from description field: 0
Templates inferred from name field: 4
Read-template multiplicity analysis:
# Reads # templates
1 4
Chemistries inferred from description field:
0 dye-primer
0 old-dye-terminator
4 big-dye-terminator
0 other
Chemistries inferred from name:
0 dye-primer
0 old-dye-terminator
0 big-dye-terminator
0 other
Directions inferred from description field:
0 fwd
0 rev
0 unknown (set to fwd)
Directions inferred from name:
0 fwd
0 rev
4 unknown (set to fwd)
Quality file: test_project.fasta.screen.qual
Input quality (quality, n_residues, %, cum, cum %, cum expected errs):
56 281 9.4 281 9.4 0.00
51 351 11.7 632 21.1 0.00
50 7 0.2 639 21.4 0.00
48 13 0.4 652 21.8 0.00
47 2 0.1 654 21.9 0.00
46 43 1.4 697 23.3 0.00
45 206 6.9 903 30.2 0.01
44 28 0.9 931 31.1 0.01
43 334 11.2 1265 42.3 0.03
42 60 2.0 1325 44.3 0.03
41 29 1.0 1354 45.3 0.04
40 284 9.5 1638 54.8 0.06
39 64 2.1 1702 56.9 0.07
38 36 1.2 1738 58.1 0.08
37 76 2.5 1814 60.7 0.09
36 19 0.6 1833 61.3 0.10
35 193 6.5 2026 67.8 0.16
34 59 2.0 2085 69.8 0.18
33 30 1.0 2115 70.8 0.20
32 111 3.7 2226 74.5 0.27
31 19 0.6 2245 75.1 0.28
30 10 0.3 2255 75.4 0.29
29 121 4.0 2376 79.5 0.44
28 17 0.6 2393 80.1 0.47
27 38 1.3 2431 81.3 0.55
26 18 0.6 2449 81.9 0.59
25 72 2.4 2521 84.3 0.82
24 46 1.5 2567 85.9 1.00
23 21 0.7 2588 86.6 1.11
22 25 0.8 2613 87.4 1.27
21 33 1.1 2646 88.5 1.53
20 18 0.6 2664 89.1 1.71
19 25 0.8 2689 90.0 2.02
18 24 0.8 2713 90.8 2.40
17 15 0.5 2728 91.3 2.70
16 23 0.8 2751 92.0 3.28
15 23 0.8 2774 92.8 4.01
14 18 0.6 2792 93.4 4.72
13 14 0.5 2806 93.9 5.43
12 20 0.7 2826 94.5 6.69
11 21 0.7 2847 95.2 8.36
10 40 1.3 2887 96.6 12.36
9 38 1.3 2925 97.9 17.14
8 26 0.9 2951 98.7 21.26
7 5 0.2 2956 98.9 22.26
6 26 0.9 2982 99.8 28.79
4 7 0.2 2989 100.0 31.58 (quality -1 = terminal quality 0)
Avg. full length: 747.2, trimmed (qual > -1): 747.2
Avg. quality: 37.7 per base
Following regions converted to N's
Exact duplicate reads: None.
Probable unremoved sequencing vector (matches excluded from assembly, quality reduced to 0): None.
Near duplicate reads: None.
Internal read matches (same orientation) : None.
No. of node-rejected pairs: None.
Multi-segment reads (initially rejected segments in parentheses) -- XXX means segments flank X'd region:
0 reads with multiple segments.
Probable deletion reads (excluded from assembly): None.
Revised quality (quality, n_residues, %, cum, cum %, cum expected errs):
90 124 4.1 124 4.1 0.00
89 14 0.5 138 4.6 0.00
88 22 0.7 160 5.4 0.00
87 14 0.5 174 5.8 0.00
86 38 1.3 212 7.1 0.00
85 28 0.9 240 8.0 0.00
84 8 0.3 248 8.3 0.00
83 16 0.5 264 8.8 0.00
82 6 0.2 270 9.0 0.00
81 16 0.5 286 9.6 0.00
80 44 1.5 330 11.0 0.00
79 8 0.3 338 11.3 0.00
78 34 1.1 372 12.4 0.00
77 32 1.1 404 13.5 0.00
76 20 0.7 424 14.2 0.00
75 58 1.9 482 16.1 0.00
74 24 0.8 506 16.9 0.00
73 22 0.7 528 17.7 0.00
72 42 1.4 570 19.1 0.00
71 33 1.1 603 20.2 0.00
70 18 0.6 621 20.8 0.00
69 28 0.9 649 21.7 0.00
68 6 0.2 655 21.9 0.00
67 35 1.2 690 23.1 0.00
66 15 0.5 705 23.6 0.00
65 7 0.2 712 23.8 0.00
64 45 1.5 757 25.3 0.00
63 12 0.4 769 25.7 0.00
62 24 0.8 793 26.5 0.00
61 29 1.0 822 27.5 0.00
60 46 1.5 868 29.0 0.00
59 24 0.8 892 29.8 0.00
58 43 1.4 935 31.3 0.00
57 15 0.5 950 31.8 0.00
56 217 7.3 1167 39.0 0.00
55 22 0.7 1189 39.8 0.00
54 14 0.5 1203 40.2 0.00
53 19 0.6 1222 40.9 0.00
52 10 0.3 1232 41.2 0.00
51 273 9.1 1505 50.4 0.00
50 14 0.5 1519 50.8 0.00
49 8 0.3 1527 51.1 0.00
48 16 0.5 1543 51.6 0.00
47 10 0.3 1553 52.0 0.00
46 32 1.1 1585 53.0 0.00
45 157 5.3 1742 58.3 0.01
44 23 0.8 1765 59.0 0.01
43 252 8.4 2017 67.5 0.02
42 20 0.7 2037 68.1 0.02
41 14 0.5 2051 68.6 0.03
40 179 6.0 2230 74.6 0.04
39 46 1.5 2276 76.1 0.05
38 14 0.5 2290 76.6 0.05
37 24 0.8 2314 77.4 0.06
36 14 0.5 2328 77.9 0.06
35 39 1.3 2367 79.2 0.07
34 16 0.5 2383 79.7 0.08
33 4 0.1 2387 79.9 0.08
32 34 1.1 2421 81.0 0.10
31 3 0.1 2424 81.1 0.10
30 5 0.2 2429 81.3 0.11
29 44 1.5 2473 82.7 0.16
28 7 0.2 2480 83.0 0.18
27 22 0.7 2502 83.7 0.22
26 11 0.4 2513 84.1 0.25
25 38 1.3 2551 85.3 0.37
24 25 0.8 2576 86.2 0.47
23 9 0.3 2585 86.5 0.51
22 12 0.4 2597 86.9 0.59
21 9 0.3 2606 87.2 0.66
20 6 0.2 2612 87.4 0.72
19 6 0.2 2618 87.6 0.79
18 9 0.3 2627 87.9 0.94
17 3 0.1 2630 88.0 1.00
16 4 0.1 2634 88.1 1.10
15 9 0.3 2643 88.4 1.38
14 3 0.1 2646 88.5 1.50
13 3 0.1 2649 88.6 1.65
12 1 0.0 2650 88.7 1.72
11 3 0.1 2653 88.8 1.95
10 5 0.2 2658 88.9 2.45
9 2 0.1 2660 89.0 2.71
8 4 0.1 2664 89.1 3.34
6 2 0.1 2666 89.2 3.84
2 71 2.4 2737 91.6 48.64
-1 252 8.4 2989 100.0 300.64 (quality -1 = terminal quality 0)
Avg. full length: 747.2, trimmed (qual > -1): 684.2
Avg. quality: 48.3 per base
LLR score histogram:
Score # cum #
15.0 1 1
LLR score histogram:
Score # cum #
15.0 1 1
2d revised quality (quality, n_residues, %, cum, cum %, cum expected errs):
90 124 4.1 124 4.1 0.00
89 14 0.5 138 4.6 0.00
88 22 0.7 160 5.4 0.00
87 14 0.5 174 5.8 0.00
86 38 1.3 212 7.1 0.00
85 28 0.9 240 8.0 0.00
84 8 0.3 248 8.3 0.00
83 16 0.5 264 8.8 0.00
82 6 0.2 270 9.0 0.00
81 16 0.5 286 9.6 0.00
80 44 1.5 330 11.0 0.00
79 8 0.3 338 11.3 0.00
78 34 1.1 372 12.4 0.00
77 32 1.1 404 13.5 0.00
76 20 0.7 424 14.2 0.00
75 58 1.9 482 16.1 0.00
74 24 0.8 506 16.9 0.00
73 22 0.7 528 17.7 0.00
72 42 1.4 570 19.1 0.00
71 33 1.1 603 20.2 0.00
70 18 0.6 621 20.8 0.00
69 28 0.9 649 21.7 0.00
68 6 0.2 655 21.9 0.00
67 35 1.2 690 23.1 0.00
66 15 0.5 705 23.6 0.00
65 7 0.2 712 23.8 0.00
64 45 1.5 757 25.3 0.00
63 12 0.4 769 25.7 0.00
62 24 0.8 793 26.5 0.00
61 29 1.0 822 27.5 0.00
60 46 1.5 868 29.0 0.00
59 24 0.8 892 29.8 0.00
58 43 1.4 935 31.3 0.00
57 15 0.5 950 31.8 0.00
56 217 7.3 1167 39.0 0.00
55 22 0.7 1189 39.8 0.00
54 14 0.5 1203 40.2 0.00
53 19 0.6 1222 40.9 0.00
52 10 0.3 1232 41.2 0.00
51 273 9.1 1505 50.4 0.00
50 14 0.5 1519 50.8 0.00
49 8 0.3 1527 51.1 0.00
48 16 0.5 1543 51.6 0.00
47 10 0.3 1553 52.0 0.00
46 32 1.1 1585 53.0 0.00
45 157 5.3 1742 58.3 0.01
44 23 0.8 1765 59.0 0.01
43 252 8.4 2017 67.5 0.02
42 20 0.7 2037 68.1 0.02
41 14 0.5 2051 68.6 0.03
40 179 6.0 2230 74.6 0.04
39 46 1.5 2276 76.1 0.05
38 14 0.5 2290 76.6 0.05
37 24 0.8 2314 77.4 0.06
36 14 0.5 2328 77.9 0.06
35 39 1.3 2367 79.2 0.07
34 16 0.5 2383 79.7 0.08
33 4 0.1 2387 79.9 0.08
32 34 1.1 2421 81.0 0.10
31 3 0.1 2424 81.1 0.10
30 5 0.2 2429 81.3 0.11
29 44 1.5 2473 82.7 0.16
28 7 0.2 2480 83.0 0.18
27 22 0.7 2502 83.7 0.22
26 11 0.4 2513 84.1 0.25
25 38 1.3 2551 85.3 0.37
24 25 0.8 2576 86.2 0.47
23 9 0.3 2585 86.5 0.51
22 12 0.4 2597 86.9 0.59
21 9 0.3 2606 87.2 0.66
20 6 0.2 2612 87.4 0.72
19 6 0.2 2618 87.6 0.79
18 9 0.3 2627 87.9 0.94
17 3 0.1 2630 88.0 1.00
16 4 0.1 2634 88.1 1.10
15 9 0.3 2643 88.4 1.38
14 3 0.1 2646 88.5 1.50
13 3 0.1 2649 88.6 1.65
12 1 0.0 2650 88.7 1.72
11 3 0.1 2653 88.8 1.95
10 5 0.2 2658 88.9 2.45
9 2 0.1 2660 89.0 2.71
8 4 0.1 2664 89.1 3.34
6 2 0.1 2666 89.2 3.84
4 1 0.0 2667 89.2 4.24
2 70 2.3 2737 91.6 48.41
-1 252 8.4 2989 100.0 300.41 (quality -1 = terminal quality 0)
Avg. full length: 747.2, trimmed (qual > -1): 684.2
Avg. quality: 48.3 per base
No. confirmed reads: 2
Avg. length: 748.5, confirmed: 671.0, str. confirmed: 670.0, trimmed: 703.0
Preliminary clone size estimate: 671 bp, depth of coverage: 2.0
Depth histogram (max_depth, #reads, cum #reads):
1 2 2
0 2 4
Forward confirmed bases: 0
Substitutions by nucleotide:
A C G T N X Z Total
A 0 0 0 0 0 0 0 0
C 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0
N 0 0 0 0 0 0 0 0
X 0 0 0 0 0 0 0 0
Z 0 0 0 0 0 0 0 0
Substitutions by quality:
0 2 3 4 5 Total
0 0 0 0 0 0 0
2 0 0 0 0 0 0
3 0 0 0 0 0 0
4 0 0 0 0 0 0
5 0 0 0 0 0 0
Histogram of spacings between adjacent indel pairs:
Reverse confirmed bases: 1408
Subs: 46 (3.27%), dels: 0 (0.00%), inserts: 0 (0.00%)
Substitutions by nucleotide:
A C G T N X Z Total
A 0 1 8 0 0 0 0 9
C 1 0 18 8 0 0 0 27
G 2 2 0 1 0 0 0 5
T 2 2 1 0 0 0 0 5
N 0 0 0 0 0 0 0 0
X 0 0 0 0 0 0 0 0
Z 0 0 0 0 0 0 0 0
Substitutions by quality:
0 2 3 4 5 Total
0 0 1 7 7 8 23
2 1 0 0 0 0 1
3 7 0 0 0 0 7
4 7 0 0 0 0 7
5 8 0 0 0 0 8
Histogram of spacings between adjacent indel pairs:
Blocked reads:
ML4924F 11 600 left
ML4924R 56 753 left
2 blocked reads: 2 left only, 0 right only, 0 both.
0 reads (not shown) lack a high-quality segment.
0 perfect duplicates
2 isolated singlets (having no non-vector match to any other read):
Read Length (# trimmed non-X bases)
ML4922R 753 (668)
ML4947F 739 (658)
Contig 1. 2 reads; 708 bp (untrimmed), 704 (trimmed). Isolated contig.
-5 728 ML4924F 628 ( 0) 3.27 0.00 0.00 9 ( 9) 21 ( 54)
C 1 763 ML4924R 703 ( 0) 0.00 0.00 0.00 0 ( 3) 55 ( 89)
Overall discrep rates (%): 1.63 0.00 0.00
Contig quality (quality, n_residues, %, cum, cum %, cum expected errs):
90 62 8.8 62 8.8 0.00
89 7 1.0 69 9.7 0.00
88 11 1.6 80 11.3 0.00
87 7 1.0 87 12.3 0.00
86 19 2.7 106 15.0 0.00
85 14 2.0 120 16.9 0.00
84 4 0.6 124 17.5 0.00
83 8 1.1 132 18.6 0.00
82 3 0.4 135 19.1 0.00
81 8 1.1 143 20.2 0.00
80 22 3.1 165 23.3 0.00
79 4 0.6 169 23.9 0.00
78 17 2.4 186 26.3 0.00
77 16 2.3 202 28.5 0.00
76 10 1.4 212 29.9 0.00
75 29 4.1 241 34.0 0.00
74 12 1.7 253 35.7 0.00
73 12 1.7 265 37.4 0.00
72 22 3.1 287 40.5 0.00
71 22 3.1 309 43.6 0.00
70 9 1.3 318 44.9 0.00
69 14 2.0 332 46.9 0.00
68 3 0.4 335 47.3 0.00
67 18 2.5 353 49.9 0.00
66 9 1.3 362 51.1 0.00
65 4 0.6 366 51.7 0.00
64 23 3.2 389 54.9 0.00
63 6 0.8 395 55.8 0.00
62 12 1.7 407 57.5 0.00
61 15 2.1 422 59.6 0.00
60 29 4.1 451 63.7 0.00
59 11 1.6 462 65.3 0.00
58 34 4.8 496 70.1 0.00
57 7 1.0 503 71.0 0.00
56 14 2.0 517 73.0 0.00
55 6 0.8 523 73.9 0.00
54 8 1.1 531 75.0 0.00
53 9 1.3 540 76.3 0.00
52 6 0.8 546 77.1 0.00
51 48 6.8 594 83.9 0.00
50 8 1.1 602 85.0 0.00
49 6 0.8 608 85.9 0.00
48 3 0.4 611 86.3 0.00
47 5 0.7 616 87.0 0.00
46 8 1.1 624 88.1 0.00
45 7 1.0 631 89.1 0.00
44 1 0.1 632 89.3 0.00
43 16 2.3 648 91.5 0.00
42 1 0.1 649 91.7 0.00
41 2 0.3 651 91.9 0.00
40 17 2.4 668 94.4 0.00
39 14 2.0 682 96.3 0.01
38 3 0.4 685 96.8 0.01
36 1 0.1 686 96.9 0.01
35 10 1.4 696 98.3 0.01
34 2 0.3 698 98.6 0.01
32 1 0.1 699 98.7 0.01
26 1 0.1 700 98.9 0.01
25 2 0.3 702 99.2 0.02
17 1 0.1 703 99.3 0.04
12 1 0.1 704 99.4 0.10
-1 4 0.6 708 100.0 4.10 (quality -1 = terminal quality 0)
Avg. full length: 708.0, trimmed (qual > -1): 704.0
Avg. quality: 65.6 per base
Initial, terminal qual 0 segments: 1-3, 708-708
Regions of LLR- adjusted quality < 2.0:
1-5, 708,
2 regions, avg size 3.0, avg spacing 354.0
First_start: 4, last_end: 674
Slack, # used pairs (max_score), unused
0 1 (15.1) 0 ( 0.0) 1
LLR histograms (used, unused pairs):
10.0 1 0
DS Gap Size Closest read (Start) Covers Read length required
now? to cover
Top strand:
left - 3 3+
708 - right 1+ ML4924F ( -5) No 713+
Bottom strand:
left - 0 0+ ML4924R ( 763) No 763+
709 - right 0+
Read/contig alignment summary, by read base; trace qualities
Qual algn cum rcum (%) unalgn X N sub del ins total (%) cum rcum (%)
56 86 86 1409 (100.00) 0 0 0 0 0 0 0 (0.00) 0 23 (1.63)
51 122 208 1323 ( 93.90) 0 0 0 0 0 0 0 (0.00) 0 23 (1.74)
50 5 213 1201 ( 85.24) 0 0 0 0 0 0 0 (0.00) 0 23 (1.92)
48 7 220 1196 ( 84.88) 0 0 0 0 0 0 0 (0.00) 0 23 (1.92)
47 2 222 1189 ( 84.39) 0 0 0 0 0 0 0 (0.00) 0 23 (1.93)
46 15 237 1187 ( 84.24) 0 0 0 0 0 0 0 (0.00) 0 23 (1.94)
45 53 290 1172 ( 83.18) 0 0 0 0 0 0 0 (0.00) 0 23 (1.96)
44 14 304 1119 ( 79.42) 0 0 0 0 0 0 0 (0.00) 0 23 (2.06)
43 98 402 1105 ( 78.42) 0 0 0 0 0 0 0 (0.00) 0 23 (2.08)
42 44 446 1007 ( 71.47) 0 0 0 0 0 0 0 (0.00) 0 23 (2.28)
41 21 467 963 ( 68.35) 0 0 0 0 0 0 0 (0.00) 0 23 (2.39)
40 99 566 942 ( 66.86) 0 0 0 0 0 0 0 (0.00) 0 23 (2.44)
39 29 595 843 ( 59.83) 0 0 0 0 0 0 0 (0.00) 0 23 (2.73)
38 26 621 814 ( 57.77) 0 0 0 0 0 0 0 (0.00) 0 23 (2.83)
37 49 670 788 ( 55.93) 0 0 0 0 0 0 0 (0.00) 0 23 (2.92)
36 8 678 739 ( 52.45) 0 0 0 0 0 0 0 (0.00) 0 23 (3.11)
35 143 821 731 ( 51.88) 0 0 0 0 0 0 0 (0.00) 0 23 (3.15)
34 28 849 588 ( 41.73) 0 0 0 0 0 0 0 (0.00) 0 23 (3.91)
33 24 873 560 ( 39.74) 0 0 0 0 0 0 0 (0.00) 0 23 (4.11)
32 64 937 536 ( 38.04) 0 0 0 0 0 0 0 (0.00) 0 23 (4.29)
31 10 947 472 ( 33.50) 0 0 0 0 0 0 0 (0.00) 0 23 (4.87)
30 6 953 462 ( 32.79) 0 0 0 0 0 0 0 (0.00) 0 23 (4.98)
29 72 1025 456 ( 32.36) 0 0 0 0 0 0 0 (0.00) 0 23 (5.04)
28 10 1035 384 ( 27.25) 0 0 0 0 0 0 0 (0.00) 0 23 (5.99)
27 19 1054 374 ( 26.54) 0 0 0 0 0 0 0 (0.00) 0 23 (6.15)
26 12 1066 355 ( 25.20) 0 0 0 0 0 0 0 (0.00) 0 23 (6.48)
25 36 1102 343 ( 24.34) 0 0 0 0 0 0 0 (0.00) 0 23 (6.71)
24 27 1129 307 ( 21.79) 0 0 0 1 0 0 1 (3.70) 1 23 (7.49)
23 13 1142 280 ( 19.87) 0 0 0 0 0 0 0 (0.00) 1 22 (7.86)
22 15 1157 267 ( 18.95) 0 0 0 0 0 0 0 (0.00) 1 22 (8.24)
21 23 1180 252 ( 17.89) 0 0 0 1 0 0 1 (4.35) 2 22 (8.73)
20 11 1191 229 ( 16.25) 0 0 0 0 0 0 0 (0.00) 2 21 (9.17)
19 12 1203 218 ( 15.47) 0 0 0 0 0 0 0 (0.00) 2 21 (9.63)
18 14 1217 206 ( 14.62) 0 0 0 0 0 0 0 (0.00) 2 21 (10.19)
17 14 1231 192 ( 13.63) 0 0 0 2 0 0 2 (14.29) 4 21 (10.94)
16 14 1245 178 ( 12.63) 0 0 0 0 0 0 0 (0.00) 4 19 (10.67)
15 20 1265 164 ( 11.64) 0 0 0 0 0 0 0 (0.00) 4 19 (11.59)
14 15 1280 144 ( 10.22) 0 0 0 2 0 0 2 (13.33) 6 19 (13.19)
13 9 1289 129 ( 9.16) 0 0 0 0 0 0 0 (0.00) 6 17 (13.18)
12 18 1307 120 ( 8.52) 0 0 0 1 0 0 1 (5.56) 7 17 (14.17)
11 17 1324 102 ( 7.24) 0 0 0 1 0 0 1 (5.88) 8 16 (15.69)
10 32 1356 85 ( 6.03) 0 0 0 5 0 0 5 (15.62) 13 15 (17.65)
9 28 1384 53 ( 3.76) 0 0 0 2 0 0 2 (7.14) 15 10 (18.87)
8 15 1399 25 ( 1.77) 0 0 0 4 0 0 4 (26.67) 19 8 (32.00)
7 2 1401 10 ( 0.71) 0 0 0 0 0 0 0 (0.00) 19 4 (40.00)
6 8 1409 8 ( 0.57) 0 0 0 4 0 0 4 (50.00) 23 4 (50.00)
-1 3 1412 0 ( 0.00) 4 0 0 0 0 0 0 (0.00) 23 0 (0.00)
Read/contig alignment summary, by read base; adjusted qualities
Qual algn cum rcum (%) unalgn X N sub del ins total (%) cum rcum (%)
90 124 124 1375 (100.00) 0 0 0 0 0 0 0 (0.00) 0 14 (1.02)
89 14 138 1251 ( 90.98) 0 0 0 0 0 0 0 (0.00) 0 14 (1.12)
88 22 160 1237 ( 89.96) 0 0 0 0 0 0 0 (0.00) 0 14 (1.13)
87 14 174 1215 ( 88.36) 0 0 0 0 0 0 0 (0.00) 0 14 (1.15)
86 38 212 1201 ( 87.35) 0 0 0 0 0 0 0 (0.00) 0 14 (1.17)
85 28 240 1163 ( 84.58) 0 0 0 0 0 0 0 (0.00) 0 14 (1.20)
84 8 248 1135 ( 82.55) 0 0 0 0 0 0 0 (0.00) 0 14 (1.23)
83 16 264 1127 ( 81.96) 0 0 0 0 0 0 0 (0.00) 0 14 (1.24)
82 6 270 1111 ( 80.80) 0 0 0 0 0 0 0 (0.00) 0 14 (1.26)
81 16 286 1105 ( 80.36) 0 0 0 0 0 0 0 (0.00) 0 14 (1.27)
80 44 330 1089 ( 79.20) 0 0 0 0 0 0 0 (0.00) 0 14 (1.29)
79 8 338 1045 ( 76.00) 0 0 0 0 0 0 0 (0.00) 0 14 (1.34)
78 34 372 1037 ( 75.42) 0 0 0 0 0 0 0 (0.00) 0 14 (1.35)
77 32 404 1003 ( 72.95) 0 0 0 0 0 0 0 (0.00) 0 14 (1.40)
76 20 424 971 ( 70.62) 0 0 0 0 0 0 0 (0.00) 0 14 (1.44)
75 58 482 951 ( 69.16) 0 0 0 0 0 0 0 (0.00) 0 14 (1.47)
74 24 506 893 ( 64.95) 0 0 0 0 0 0 0 (0.00) 0 14 (1.57)
73 22 528 869 ( 63.20) 0 0 0 0 0 0 0 (0.00) 0 14 (1.61)
72 42 570 847 ( 61.60) 0 0 0 0 0 0 0 (0.00) 0 14 (1.65)
71 33 603 805 ( 58.55) 0 0 0 0 0 0 0 (0.00) 0 14 (1.74)
70 18 621 772 ( 56.15) 0 0 0 0 0 0 0 (0.00) 0 14 (1.81)
69 28 649 754 ( 54.84) 0 0 0 0 0 0 0 (0.00) 0 14 (1.86)
68 6 655 726 ( 52.80) 0 0 0 0 0 0 0 (0.00) 0 14 (1.93)
67 35 690 720 ( 52.36) 0 0 0 0 0 0 0 (0.00) 0 14 (1.94)
66 15 705 685 ( 49.82) 0 0 0 0 0 0 0 (0.00) 0 14 (2.04)
65 7 712 670 ( 48.73) 0 0 0 0 0 0 0 (0.00) 0 14 (2.09)
64 45 757 663 ( 48.22) 0 0 0 0 0 0 0 (0.00) 0 14 (2.11)
63 12 769 618 ( 44.95) 0 0 0 0 0 0 0 (0.00) 0 14 (2.27)
62 24 793 606 ( 44.07) 0 0 0 0 0 0 0 (0.00) 0 14 (2.31)
61 29 822 582 ( 42.33) 0 0 0 0 0 0 0 (0.00) 0 14 (2.41)
60 46 868 553 ( 40.22) 0 0 0 0 0 0 0 (0.00) 0 14 (2.53)
59 24 892 507 ( 36.87) 0 0 0 0 0 0 0 (0.00) 0 14 (2.76)
58 43 935 483 ( 35.13) 0 0 0 0 0 0 0 (0.00) 0 14 (2.90)
57 15 950 440 ( 32.00) 0 0 0 0 0 0 0 (0.00) 0 14 (3.18)
56 24 974 425 ( 30.91) 0 0 0 0 0 0 0 (0.00) 0 14 (3.29)
55 22 996 401 ( 29.16) 0 0 0 0 0 0 0 (0.00) 0 14 (3.49)
54 14 1010 379 ( 27.56) 0 0 0 0 0 0 0 (0.00) 0 14 (3.69)
53 19 1029 365 ( 26.55) 0 0 0 0 0 0 0 (0.00) 0 14 (3.84)
52 10 1039 346 ( 25.16) 0 0 0 0 0 0 0 (0.00) 0 14 (4.05)
51 52 1091 336 ( 24.44) 0 0 0 0 0 0 0 (0.00) 0 14 (4.17)
50 12 1103 284 ( 20.65) 0 0 0 0 0 0 0 (0.00) 0 14 (4.93)
49 8 1111 272 ( 19.78) 0 0 0 0 0 0 0 (0.00) 0 14 (5.15)
48 10 1121 264 ( 19.20) 0 0 0 0 0 0 0 (0.00) 0 14 (5.30)
47 10 1131 254 ( 18.47) 0 0 0 0 0 0 0 (0.00) 0 14 (5.51)
46 9 1140 244 ( 17.75) 0 0 0 0 0 0 0 (0.00) 0 14 (5.74)
45 8 1148 235 ( 17.09) 0 0 0 0 0 0 0 (0.00) 0 14 (5.96)
44 9 1157 227 ( 16.51) 0 0 0 0 0 0 0 (0.00) 0 14 (6.17)
43 17 1174 218 ( 15.85) 0 0 0 0 0 0 0 (0.00) 0 14 (6.42)
42 4 1178 201 ( 14.62) 0 0 0 0 0 0 0 (0.00) 0 14 (6.97)
41 6 1184 197 ( 14.33) 0 0 0 0 0 0 0 (0.00) 0 14 (7.11)
40 31 1215 191 ( 13.89) 0 0 0 0 0 0 0 (0.00) 0 14 (7.33)
39 25 1240 160 ( 11.64) 0 0 0 0 0 0 0 (0.00) 0 14 (8.75)
38 5 1245 135 ( 9.82) 0 0 0 0 0 0 0 (0.00) 0 14 (10.37)
36 3 1248 130 ( 9.45) 0 0 0 0 0 0 0 (0.00) 0 14 (10.77)
35 16 1264 127 ( 9.24) 0 0 0 0 0 0 0 (0.00) 0 14 (11.02)
34 4 1268 111 ( 8.07) 0 0 0 0 0 0 0 (0.00) 0 14 (12.61)
33 2 1270 107 ( 7.78) 0 0 0 0 0 0 0 (0.00) 0 14 (13.08)
32 1 1271 105 ( 7.64) 0 0 0 0 0 0 0 (0.00) 0 14 (13.33)
31 2 1273 104 ( 7.56) 0 0 0 0 0 0 0 (0.00) 0 14 (13.46)
29 4 1277 102 ( 7.42) 0 0 0 0 0 0 0 (0.00) 0 14 (13.73)
28 2 1279 98 ( 7.13) 0 0 0 0 0 0 0 (0.00) 0 14 (14.29)
27 2 1281 96 ( 6.98) 0 0 0 0 0 0 0 (0.00) 0 14 (14.58)
26 4 1285 94 ( 6.84) 0 0 0 0 0 0 0 (0.00) 0 14 (14.89)
25 7 1292 90 ( 6.55) 0 0 0 0 0 0 0 (0.00) 0 14 (15.56)
24 9 1301 83 ( 6.04) 0 0 0 0 0 0 0 (0.00) 0 14 (16.87)
23 1 1302 74 ( 5.38) 0 0 0 0 0 0 0 (0.00) 0 14 (18.92)
22 2 1304 73 ( 5.31) 0 0 0 0 0 0 0 (0.00) 0 14 (19.18)
21 3 1307 71 ( 5.16) 0 0 0 1 0 0 1 (33.33) 1 14 (19.72)
20 1 1308 68 ( 4.95) 0 0 0 0 0 0 0 (0.00) 1 13 (19.12)
17 4 1312 67 ( 4.87) 0 0 0 1 0 0 1 (25.00) 2 13 (19.40)
16 1 1313 63 ( 4.58) 0 0 0 0 0 0 0 (0.00) 2 12 (19.05)
15 6 1319 62 ( 4.51) 0 0 0 0 0 0 0 (0.00) 2 12 (19.35)
14 1 1320 56 ( 4.07) 0 0 0 0 0 0 0 (0.00) 2 12 (21.43)
13 3 1323 55 ( 4.00) 0 0 0 0 0 0 0 (0.00) 2 12 (21.82)
12 5 1328 52 ( 3.78) 0 0 0 0 0 0 0 (0.00) 2 12 (23.08)
11 10 1338 47 ( 3.42) 0 0 0 1 0 0 1 (10.00) 3 12 (25.53)
10 11 1349 37 ( 2.69) 0 0 0 4 0 0 4 (36.36) 7 11 (29.73)
9 13 1362 26 ( 1.89) 0 0 0 2 0 0 2 (15.38) 9 7 (26.92)
8 9 1371 13 ( 0.95) 0 0 0 3 0 0 3 (33.33) 12 5 (38.46)
6 4 1375 4 ( 0.29) 0 0 0 2 0 0 2 (50.00) 14 2 (50.00)
-1 37 1412 0 ( 0.00) 4 0 0 9 0 0 9 (24.32) 23 0 (0.00)
Depth 0 regions:
Block histogram:
Qual bases cum blocks
0 4 4 2
12 1 5 2
17 1 6 2
25 2 8 3
26 1 9 3
32 1 10 2
34 2 12 2
35 10 22 5
36 1 23 6
38 3 26 7
39 14 40 9
40 17 57 9
41 2 59 10
42 1 60 11
43 16 76 15
44 1 77 14
45 7 84 15
46 8 92 16
47 5 97 18
48 3 100 19
49 6 106 21
50 8 114 24
51 48 162 21
52 6 168 21
53 9 177 23
54 8 185 23
55 6 191 24
56 14 205 22
57 7 212 23
58 34 246 29
59 11 257 28
60 29 286 30
61 15 301 32
62 12 313 29
63 6 319 30
64 23 342 24
65 4 346 24
66 9 355 23
67 18 373 25
68 3 376 26
69 14 390 30
70 9 399 29
71 22 421 30
72 22 443 32
73 12 455 30
74 12 467 33
75 29 496 32
76 10 506 30
77 16 522 33
78 17 539 30
79 4 543 30
80 22 565 29
81 8 573 27
82 3 576 27
83 8 584 25
84 4 588 24
85 14 602 25
86 19 621 26
87 7 628 27
88 11 639 20
89 7 646 17
90 62 708 1
SS region: 4 (0.56%), flagged: 0 (0.00%)
Sites with total LLR scores < -3.0 [max pos LLR read, max neg LLR read] (#discrep top reads, #discrep bottom reads): None.
Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.
Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.
Gaps in unique-read coverage: None.
Subclone/read contig links and consistency checks (* = inconsistency; Contig 0 = singlets)
Max subclone size: 5000
Size histogram for consistent forward-reverse pairs (*** = inconsistent pairs)
*** 0
Consistent opp sense links (* = not used in chain, ** = multiple non-zero):