BRESEQ :: Summary Statistics

breseq version 0.35.7 revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

	read file	reads	bases	passed filters	average	longest	mapped
errors	SRR2584534_1	1,720,420	173,762,420	100.0%	101.0 bases	101 bases	84.8%
errors	SRR2584534_2	1,720,414	173,761,814	100.0%	101.0 bases	101 bases	84.2%
	total	3,440,834	347,524,234	100.0%	101.0 bases	101 bases	84.5%

Reference Sequence Information

		seq id	length	fit mean	fit dispersion	% mapped reads	description
coverage	distribution	1	108,051	66.2	2.6	2.5%	na
coverage	distribution	2	103,027	59.3	2.4	2.1%	na
coverage	distribution	3	80,514	63.0	2.6	1.8%	na
coverage	distribution	4	78,067	56.9	2.7	1.6%	na
coverage	distribution	5	64,881	62.3	3.3	1.6%	na
coverage	distribution	6	60,364	62.4	1.8	1.3%	na
coverage	distribution	7	59,421	55.0	1.7	1.2%	na
coverage	distribution	8	56,436	56.7	2.8	1.1%	na
coverage	distribution	9	56,279	70.1	2.1	1.4%	na
coverage	distribution	10	54,363	67.1	1.9	1.3%	na
coverage	distribution	11	54,219	61.7	2.5	1.2%	na
coverage	distribution	12	53,253	66.3	2.2	1.2%	na
coverage	distribution	13	52,198	72.4	3.6	1.4%	na
coverage	distribution	14	52,173	77.0	3.4	1.4%	na
coverage	distribution	15	49,040	64.5	2.2	0.6%	na
coverage	distribution	16	47,700	68.8	3.0	1.2%	na
coverage	distribution	17	46,866	69.4	3.1	1.1%	na
coverage	distribution	18	44,693	59.1	1.9	0.9%	na
coverage	distribution	19	43,912	63.2	1.7	1.0%	na
coverage	distribution	20	43,865	65.0	2.7	1.0%	na
coverage	distribution	21	41,893	63.3	1.7	0.9%	na
coverage	distribution	22	41,696	65.0	3.0	0.9%	na
coverage	distribution	23	41,186	73.3	1.9	1.0%	na
coverage	distribution	24	40,740	64.3	2.1	0.7%	na
coverage	distribution	25	39,931	55.0	2.3	0.8%	na
coverage	distribution	26	39,746	65.7	4.3	0.9%	na
coverage	distribution	27	39,041	70.1	2.0	1.0%	na
coverage	distribution	28	36,827	63.7	2.0	0.9%	na
coverage	distribution	29	35,867	70.1	3.0	0.9%	na
coverage	distribution	30	35,266	101.1	3.2	1.2%	na
coverage	distribution	31	34,016	67.0	3.1	0.8%	na
coverage	distribution	32	33,900	72.2	2.5	0.8%	na
coverage	distribution	33	33,871	59.6	2.5	0.7%	na
coverage	distribution	34	33,761	72.9	2.7	0.9%	na
coverage	distribution	35	33,599	66.4	2.1	0.8%	na
coverage	distribution	36	33,227	66.7	2.3	0.8%	na
coverage	distribution	37	32,985	57.7	1.6	0.7%	na
coverage	distribution	38	32,819	59.5	2.6	0.7%	na
coverage	distribution	39	32,802	55.0	1.7	0.6%	na
coverage	distribution	40	32,569	63.6	2.4	0.7%	na
coverage	distribution	41	32,291	67.8	2.5	0.8%	na
coverage	distribution	42	32,020	71.9	2.9	0.9%	na
coverage	distribution	43	31,196	59.5	2.0	0.7%	na
coverage	distribution	44	31,078	69.6	2.4	0.8%	na
coverage	distribution	45	30,869	76.4	2.5	0.8%	na
coverage	distribution	46	30,710	57.1	2.4	0.6%	na
coverage	distribution	47	30,112	69.0	2.8	0.8%	na
coverage	distribution	48	29,957	60.1	1.7	0.6%	na
coverage	distribution	49	29,908	64.0	2.1	0.7%	na
coverage	distribution	50	29,744	69.0	2.8	0.7%	na
coverage	distribution	51	29,294	66.2	1.6	0.4%	na
coverage	distribution	52	29,257	58.6	1.9	0.6%	na
coverage	distribution	53	29,077	67.3	2.6	0.7%	na
coverage	distribution	54	28,773	60.5	1.9	0.6%	na
coverage	distribution	55	27,005	63.1	2.1	0.6%	na
coverage	distribution	56	26,090	56.0	1.9	0.5%	na
coverage	distribution	57	26,063	57.6	1.7	0.5%	na
coverage	distribution	58	26,029	68.7	1.7	0.6%	na
coverage	distribution	59	25,090	53.6	1.8	0.5%	na
coverage	distribution	60	24,693	59.0	2.6	0.5%	na
coverage	distribution	61	24,668	70.3	1.6	0.6%	na
coverage	distribution	62	24,568	65.1	2.5	0.6%	na
coverage	distribution	63	24,466	57.2	2.1	0.5%	na
coverage	distribution	64	23,955	63.3	2.4	0.5%	na
coverage	distribution	65	23,905	101.8	2.1	0.9%	na
coverage	distribution	66	23,726	57.4	1.8	0.5%	na
coverage	distribution	67	23,717	65.5	1.9	0.5%	na
coverage	distribution	68	23,344	60.6	2.1	0.5%	na
coverage	distribution	69	23,343	62.2	1.9	0.4%	na
coverage	distribution	70	22,849	61.4	2.1	0.5%	na
coverage	distribution	71	22,716	62.3	3.4	0.5%	na
coverage	distribution	72	22,438	62.1	1.8	0.5%	na
coverage	distribution	73	22,246	70.6	3.9	0.6%	na
coverage	distribution	74	22,019	57.6	1.9	0.4%	na
coverage	distribution	75	21,857	69.8	2.9	0.6%	na
coverage	distribution	76	21,559	61.6	1.9	0.5%	na
coverage	distribution	77	21,347	55.9	2.0	0.4%	na
coverage	distribution	78	21,310	62.2	2.6	0.5%	na
coverage	distribution	79	21,233	65.2	2.6	0.5%	na
coverage	distribution	80	21,134	54.7	2.2	0.4%	na
coverage	distribution	81	20,057	63.4	2.3	0.5%	na
coverage	distribution	82	19,979	81.2	2.6	0.2%	na
coverage	distribution	83	19,766	0.8	1.0	0.0%	na
coverage	distribution	84	19,746	60.0	2.0	0.4%	na
coverage	distribution	85	19,737	64.4	2.1	0.4%	na
coverage	distribution	86	19,585	65.3	2.7	0.5%	na
coverage	distribution	87	19,524	57.4	2.9	0.4%	na
coverage	distribution	88	19,252	64.4	1.9	0.4%	na
coverage	distribution	89	18,552	59.8	1.7	0.4%	na
coverage	distribution	90	18,370	58.4	2.1	0.4%	na
coverage	distribution	91	18,160	60.6	1.8	0.4%	na
coverage	distribution	92	17,887	1.1	1.0	0.0%	na
coverage	distribution	93	17,731	58.2	1.7	0.4%	na
coverage	distribution	94	17,606	67.9	2.6	0.4%	na
coverage	distribution	95	17,232	66.5	2.2	0.4%	na
coverage	distribution	96	17,144	55.8	1.8	0.3%	na
coverage	distribution	97	17,078	60.6	2.1	0.4%	na
coverage	distribution	98	17,037	63.9	2.6	0.4%	na
coverage	distribution	99	16,584	53.4	1.9	0.3%	na
coverage	distribution	100	16,396	58.4	1.8	0.3%	na
coverage	distribution	101	16,326	58.8	3.1	0.3%	na
coverage	distribution	102	16,281	57.9	2.6	0.3%	na
coverage	distribution	103	16,246	50.3	1.6	0.3%	na
coverage	distribution	104	16,231	60.3	1.4	0.3%	na
coverage	distribution	105	15,857	62.1	2.3	0.3%	na
coverage	distribution	106	15,781	56.8	2.0	0.3%	na
coverage	distribution	107	15,491	73.3	2.9	0.4%	na
coverage	distribution	108	15,407	77.0	2.8	0.4%	na
coverage	distribution	109	15,277	60.1	2.7	0.3%	na
coverage	distribution	110	15,236	67.9	1.9	0.4%	na
coverage	distribution	111	14,721	70.0	2.1	0.4%	na
coverage	distribution	112	14,615	64.5	2.3	0.3%	na
coverage	distribution	113	14,540	55.1	1.7	0.3%	na
coverage	distribution	114	14,464	75.5	3.0	0.4%	na
coverage	distribution	115	14,429	66.9	2.4	0.3%	na
coverage	distribution	116	14,374	70.3	2.6	0.3%	na
coverage	distribution	117	14,361	53.0	2.2	0.3%	na
coverage	distribution	118	14,204	64.5	2.3	0.3%	na
coverage	distribution	119	14,156	53.7	2.8	0.3%	na
coverage	distribution	120	14,144	74.2	3.0	0.4%	na
coverage	distribution	121	14,106	59.7	2.5	0.3%	na
coverage	distribution	122	14,076	58.2	1.4	0.3%	na
coverage	distribution	123	14,064	57.1	1.9	0.3%	na
coverage	distribution	124	13,852	63.0	2.2	0.3%	na
coverage	distribution	125	13,803	69.2	4.8	0.4%	na
coverage	distribution	126	13,694	66.0	2.6	0.3%	na
coverage	distribution	127	13,634	67.3	1.7	0.3%	na
coverage	distribution	128	13,426	69.6	2.0	0.3%	na
coverage	distribution	129	13,398	57.6	2.0	0.3%	na
coverage	distribution	130	13,205	NA	NA	0.0%	na
coverage	distribution	131	13,095	69.7	2.9	0.3%	na
coverage	distribution	132	13,049	65.0	2.1	0.3%	na
coverage	distribution	133	13,039	62.3	4.0	0.3%	na
coverage	distribution	134	12,836	66.9	2.0	0.3%	na
coverage	distribution	135	12,670	76.7	1.9	0.3%	na
coverage	distribution	136	12,424	58.6	1.8	0.2%	na
coverage	distribution	137	12,181	72.9	3.4	0.3%	na
coverage	distribution	138	11,857	69.9	1.6	0.3%	na
coverage	distribution	139	11,822	55.4	1.8	0.2%	na
coverage	distribution	140	11,485	61.4	2.2	0.2%	na
coverage	distribution	141	11,390	66.6	1.7	0.3%	na
coverage	distribution	142	11,221	58.7	1.7	0.2%	na
coverage	distribution	143	10,889	59.1	1.6	0.2%	na
coverage	distribution	144	10,516	57.3	2.2	0.2%	na
coverage	distribution	145	10,378	61.8	2.0	0.2%	na
coverage	distribution	146	10,176	57.8	3.0	0.2%	na
coverage	distribution	147	9,954	74.8	2.8	0.3%	na
coverage	distribution	148	9,904	65.3	2.2	0.2%	na
coverage	distribution	149	9,895	59.7	2.0	0.2%	na
coverage	distribution	150	9,892	61.5	2.2	0.2%	na
coverage	distribution	151	9,732	66.8	2.0	0.2%	na
coverage	distribution	152	9,680	65.4	3.8	0.2%	na
coverage	distribution	153	9,642	58.7	2.9	0.2%	na
coverage	distribution	154	9,582	62.3	1.7	0.2%	na
coverage	distribution	155	9,554	55.6	2.0	0.2%	na
coverage	distribution	156	9,528	57.7	1.9	0.2%	na
coverage	distribution	157	9,373	70.5	3.5	0.2%	na
coverage	distribution	158	9,359	70.1	2.1	0.2%	na
coverage	distribution	159	8,925	56.2	2.2	0.2%	na
coverage	distribution	160	8,899	54.7	1.4	0.2%	na
coverage	distribution	161	8,872	62.7	2.8	0.2%	na
coverage	distribution	162	8,767	62.3	2.8	0.2%	na
coverage	distribution	163	8,564	58.4	1.3	0.2%	na
coverage	distribution	164	8,502	0.7	1.0	0.0%	na
coverage	distribution	165	8,501	56.5	1.2	0.2%	na
coverage	distribution	166	8,398	75.1	2.1	0.2%	na
coverage	distribution	167	8,289	76.9	1.2	0.1%	na
coverage	distribution	168	8,158	59.9	2.2	0.2%	na
coverage	distribution	169	7,848	NA	NA	0.0%	na
coverage	distribution	170	7,767	59.4	1.7	0.2%	na
coverage	distribution	171	7,707	68.4	2.3	0.2%	na
coverage	distribution	172	7,705	64.3	1.9	0.2%	na
coverage	distribution	173	7,637	59.0	1.5	0.2%	na
coverage	distribution	174	7,466	56.7	1.8	0.1%	na
coverage	distribution	175	7,365	61.5	1.6	0.2%	na
coverage	distribution	176	7,365	61.2	1.7	0.2%	na
coverage	distribution	177	7,332	58.8	3.4	0.1%	na
coverage	distribution	178	7,327	57.4	1.6	0.1%	na
coverage	distribution	179	7,204	68.9	2.3	0.2%	na
coverage	distribution	180	7,195	57.5	1.2	0.1%	na
coverage	distribution	181	6,978	71.0	2.2	0.2%	na
coverage	distribution	182	6,967	65.6	1.4	0.2%	na
coverage	distribution	183	6,872	79.9	1.7	0.8%	na
coverage	distribution	184	6,777	65.3	2.6	0.2%	na
coverage	distribution	185	6,771	77.4	4.3	0.2%	na
coverage	distribution	186	6,614	78.4	4.2	0.2%	na
coverage	distribution	187	6,592	82.0	3.1	0.2%	na
coverage	distribution	188	6,383	47.1	1.5	0.1%	na
coverage	distribution	189	6,363	55.4	1.5	0.1%	na
coverage	distribution	190	6,342	61.3	1.3	0.1%	na
coverage	distribution	191	5,864	73.1	3.0	0.2%	na
coverage	distribution	192	5,790	55.9	2.4	0.1%	na
coverage	distribution	193	5,681	0.5	1.0	0.0%	na
coverage	distribution	194	5,424	62.4	1.6	0.1%	na
coverage	distribution	195	5,423	57.8	2.3	0.1%	na
coverage	distribution	196	5,276	52.4	2.0	0.1%	na
coverage	distribution	197	5,170	65.8	1.4	0.1%	na
coverage	distribution	198	5,050	65.2	1.2	0.1%	na
coverage	distribution	199	4,737	74.6	1.2	0.1%	na
coverage	distribution	200	4,567	49.3	2.4	0.1%	na
coverage	distribution	201	4,520	80.4	3.3	0.1%	na
coverage	distribution	202	4,399	60.7	2.3	0.1%	na
coverage	distribution	203	4,306	49.3	2.1	0.1%	na
coverage	distribution	204	4,218	70.9	2.1	0.1%	na
coverage	distribution	205	4,123	65.6	2.4	0.1%	na
coverage	distribution	206	4,098	76.0	3.2	0.1%	na
coverage	distribution	207	3,729	49.2	1.6	0.1%	na
coverage	distribution	208	3,676	NA	NA	0.0%	na
coverage	distribution	209	3,401	59.9	1.2	0.1%	na
coverage	distribution	210	2,923	58.1	1.5	0.1%	na
coverage	distribution	211	2,719	87.8	5.7	0.1%	na
coverage	distribution	212	2,487	57.7	1.2	0.1%	na
coverage	distribution	213	2,456	95.1	9.0	0.1%	na
coverage	distribution	214	2,433	NA	NA	0.0%	na
coverage	distribution	215	2,341	58.2	1.3	0.0%	na
coverage	distribution	216	2,311	79.9	3.1	0.1%	na
coverage	distribution	217	2,224	NA	NA	0.0%	na
coverage	distribution	218	1,999	57.9	1.3	0.0%	na
coverage	distribution	219	1,818	691.6	31.2	0.4%	na
coverage	distribution	220	1,766	66.1	1.5	0.0%	na
coverage	distribution	221	1,707	115.2	1.3	0.1%	na
coverage	distribution	222	1,443	3090.6	14.5	1.4%	na
coverage	distribution	223	698	1871.3	4.8	0.4%	na
coverage	distribution	224	660	58.1	1.5	0.0%	na
coverage	distribution	225	280	490.1	6.6	0.0%	na
coverage	distribution	226	238	90.6	6.4	0.0%	na
coverage	distribution	227	188	551.0	6.5	0.0%	na
		total	4,445,260			100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.

New Junction Evidence

Junction Candidates Tested

option	limit	actual
Number of alignment pairs examined for constructing junction candidates	≤ 100000	74515
Coverage evenness (position-hash) score of junction candidates	≥ 2	≥ 6
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold	100 ≤ n ≤ 5000	2138
Total length of all junction candidates (factor times the reference genome length)	≤ 0.1	0.097

Junction Skew Score Calculation

reference sequence	pr(no read start)
1	0.73330
2	0.75810
3	0.74584
4	0.76181
5	0.74036
6	0.74884
7	0.76948
8	0.76301
9	0.72594
10	0.73065
11	0.74848
12	0.73429
13	0.70725
14	0.69580
15	0.86710
16	0.72434
17	0.72814
18	0.75922
19	0.74650
20	0.73113
21	0.73937
22	0.75879
23	0.71522
24	0.80054
25	0.77367
26	0.73297
27	0.72370
28	0.73483
29	0.70651
30	0.63373
31	0.72603
32	0.72094
33	0.75680
34	0.71058
35	0.73688
36	0.72440
37	0.76558
38	0.75782
39	0.77492
40	0.74229
41	0.72734
42	0.70003
43	0.75442
44	0.72472
45	0.70236
46	0.76472
47	0.71757
48	0.75268
49	0.74360
50	0.71702
51	0.85811
52	0.75884
53	0.73078
54	0.75479
55	0.74151
56	0.76941
57	0.76399
58	0.72440
59	0.77770
60	0.76096
61	0.71727
62	0.71732
63	0.76183
64	0.74521
65	0.62945
66	0.76414
67	0.73705
68	0.75932
69	0.78647
70	0.74977
71	0.74342
72	0.75381
73	0.71772
74	0.76230
75	0.71128
76	0.75215
77	0.76732
78	0.72755
79	0.73098
80	0.77707
81	0.73997
82	0.87126
83	0.98621
84	0.75750
85	0.74054
86	0.73541
87	0.76478
88	0.74374
89	0.76299
90	0.75659
91	0.75146
92	0.98935
93	0.76310
94	0.73075
95	0.73369
96	0.77024
97	0.75146
98	0.74649
99	0.77713
100	0.76113
101	0.76305
102	0.76098
103	0.79170
104	0.75359
105	0.74532
106	0.77061
107	0.70218
108	0.70218
109	0.75741
110	0.72050
111	0.73382
112	0.74359
113	0.76974
114	0.70727
115	0.73501
116	0.72546
117	0.77686
118	0.73764
119	0.77098
120	0.70662
121	0.75872
122	0.76701
123	0.76280
124	0.74708
125	0.70003
126	0.73295
127	0.73225
128	0.72363
129	0.76015
130	0.99826
131	0.72073
132	0.73347
133	0.71731
134	0.73232
135	0.70367
136	0.76578
137	0.71361
138	0.72345
139	0.77491
140	0.75603
141	0.73464
142	0.76709
143	0.75875
144	0.76850
145	0.74860
146	0.74671
147	0.70449
148	0.73889
149	0.75836
150	0.75708
151	0.74255
152	0.74690
153	0.74761
154	0.74468
155	0.77292
156	0.76789
157	0.73056
158	0.72321
159	0.77350
160	0.77587
161	0.73259
162	0.75471
163	0.76045
164	0.99065
165	0.77150
166	0.72017
167	0.92309
168	0.75956
169	0.99694
170	0.75969
171	0.73427
172	0.74692
173	0.76823
174	0.77203
175	0.75580
176	0.75336
177	0.76637
178	0.81957
179	0.73105
180	0.76810
181	0.71303
182	0.74315
183	0.43997
184	0.72731
185	0.74310
186	0.69308
187	0.74393
188	0.79665
189	0.77424
190	0.75859
191	0.70891
192	0.75725
193	0.98733
194	0.74723
195	0.77264
196	0.79113
197	0.74458
198	0.74277
199	0.71332
200	0.80053
201	0.71084
202	0.75926
203	0.79587
204	0.72807
205	0.74169
206	0.70766
207	0.78426
208	0.99646
209	0.76345
210	0.77335
211	0.68408
212	0.74306
213	0.69951
214	0.99671
215	0.76036
216	0.70532
217	0.99505
218	0.77414
219	0.19939
220	0.74632
221	0.61306
222	0.06895
223	0.14685
224	0.80303
225	0.48036
226	0.78782
227	0.57979

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

option	value
Coverage evenness (position-hash) score of predicted junctions must be	≥ 3
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction	0.1
Junction allow suboptimal matches	FALSE
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be	≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction	≥ 1

Read Alignment Evidence

option	value
Mode	Consensus/Mixed Base
Ploidy	1 (haploid)
Consensus mutation E-value cutoff	10
Consensus frequency cutoff	0.8
Consensus minimum variant coverage each strand	OFF
Consensus minimum total coverage each strand	OFF
Consensus minimum variant coverage	OFF
Consensus minimum total coverage	OFF
Polymorphism E-value cutoff	10
Polymorphism frequency cutoff	0.2
Polymorphism minimum variant coverage each strand	OFF
Polymorphism minimum total coverage each strand	OFF
Polymorphism minimum variant coverage	OFF
Polymorphism minimum total coverage	OFF
Polymorphism bias cutoff	OFF
Predict indel polymorphisms	YES
Skip indel polymorphisms in homopolymers runs of	OFF
Skip base substitutions when they create a homopolymer flanked on each side by	OFF

Software Versions

program	version
bowtie2	2.3.4.1
R	4.0.0

Execution Times

step	start	end	elapsed
Read and reference sequence file input	10:33:48 20 Jul 2021	10:35:32 20 Jul 2021	1 minute 44 seconds
Read alignment to reference genome	10:35:32 20 Jul 2021	10:38:00 20 Jul 2021	2 minutes 28 seconds
Preprocessing alignments for candidate junction identification	10:38:00 20 Jul 2021	10:39:22 20 Jul 2021	1 minute 22 seconds
Preliminary analysis of coverage distribution	10:39:22 20 Jul 2021	10:42:30 20 Jul 2021	3 minutes 8 seconds
Identifying junction candidates	10:42:30 20 Jul 2021	10:50:58 20 Jul 2021	8 minutes 28 seconds
Re-alignment to junction candidates	10:50:58 20 Jul 2021	10:51:26 20 Jul 2021	28 seconds
Resolving best read alignments	10:51:26 20 Jul 2021	10:53:12 20 Jul 2021	1 minute 46 seconds
Creating BAM files	10:53:12 20 Jul 2021	10:54:05 20 Jul 2021	53 seconds
Tabulating error counts	10:54:05 20 Jul 2021	10:54:30 20 Jul 2021	25 seconds
Re-calibrating base error rates	10:54:30 20 Jul 2021	10:55:56 20 Jul 2021	1 minute 26 seconds
Examining read alignment evidence	10:55:56 20 Jul 2021	10:58:51 20 Jul 2021	2 minutes 55 seconds
Polymorphism statistics	10:58:51 20 Jul 2021	10:58:52 20 Jul 2021	1 second
Output	10:58:52 20 Jul 2021	11:00:58 20 Jul 2021	2 minutes 6 seconds
Output :: Mutation Prediction	10:58:52 20 Jul 2021	10:58:59 20 Jul 2021	7 seconds
Output :: Mutation Annotation	10:58:59 20 Jul 2021	10:59:00 20 Jul 2021	1 second
Total			27 minutes 18 seconds