#=GENOME_DIFF	1.0
RA	21	.	CP028101	216976	0	T	G	bias_e_value=8.49646e-21	bias_p_value=3.89728e-27	consensus_reject=FREQUENCY_CUTOFF	consensus_score=619.9	fisher_strand_p_value=5.90505e-29	frequency=2.500e-01	ks_quality_p_value=1	major_base=T	major_cov=35/133	major_frequency=7.500e-01	minor_base=G	minor_cov=56/0	new_cov=56/0	polymorphism_frequency=2.500e-01	polymorphism_score=27.3	prediction=polymorphism	ref_cov=35/133	total_cov=93/133
RA	22	.	CP028101	336797	0	A	T	consensus_score=61.7	frequency=1	major_base=T	major_cov=20/11	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=20/11	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=20/11
RA	23	.	CP028101	336797	1	.	T	bias_e_value=1575090	bias_p_value=0.722484	consensus_score=63.8	fisher_strand_p_value=0.354839	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=20/10	major_frequency=9.677e-01	minor_base=.	minor_cov=0/1	new_cov=20/10	polymorphism_frequency=9.677e-01	polymorphism_score=-2.8	prediction=consensus	ref_cov=0/1	total_cov=20/11
RA	24	.	CP028101	336797	2	.	T	bias_e_value=843307	bias_p_value=0.38682	consensus_score=61.7	fisher_strand_p_value=0.354839	frequency=1	ks_quality_p_value=0.354839	major_base=T	major_cov=20/10	major_frequency=9.677e-01	minor_base=.	minor_cov=0/1	new_cov=20/10	polymorphism_frequency=9.677e-01	polymorphism_score=-2.8	prediction=consensus	ref_cov=0/1	total_cov=20/11
RA	25	.	CP028101	516032	0	G	A	consensus_score=424.2	frequency=1	major_base=A	major_cov=60/44	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=60/44	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=60/44
RA	26	.	CP028101	618209	0	C	G	bias_e_value=1650120	bias_p_value=0.756899	consensus_reject=FREQUENCY_CUTOFF	consensus_score=166.4	fisher_strand_p_value=0.432929	frequency=6.593e-01	ks_quality_p_value=0.900035	major_base=G	major_cov=96/142	major_frequency=6.593e-01	minor_base=C	minor_cov=55/68	new_cov=96/142	polymorphism_frequency=6.593e-01	polymorphism_score=inf	prediction=polymorphism	ref_cov=55/68	total_cov=151/211
RA	27	.	CP028101	693938	0	C	T	bias_e_value=2180100	bias_p_value=1	consensus_score=115.8	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=30/16	major_frequency=9.787e-01	minor_base=C	minor_cov=1/0	new_cov=30/16	polymorphism_frequency=9.787e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=32/16
RA	28	.	CP028101	693972	0	G	A	consensus_score=41.2	frequency=1	major_base=A	major_cov=12/8	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=12/8	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=12/8
RA	29	.	CP028101	761017	0	A	G	consensus_score=68.1	frequency=1	major_base=G	major_cov=10/9	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=10/9	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=10/9
RA	30	.	CP028101	761062	0	A	G	consensus_score=124.6	frequency=1	major_base=G	major_cov=18/15	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=18/15	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=18/15
RA	31	.	CP028101	875381	0	A	G	bias_e_value=794560	bias_p_value=0.36446	consensus_score=155.4	fisher_strand_p_value=0.392157	frequency=1	ks_quality_p_value=0.294118	major_base=G	major_cov=19/31	major_frequency=9.804e-01	minor_base=A	minor_cov=1/0	new_cov=19/31	polymorphism_frequency=9.804e-01	polymorphism_score=-3.6	prediction=consensus	ref_cov=1/0	total_cov=20/31
RA	32	.	CP028101	880783	0	A	G	consensus_score=150.0	frequency=1	major_base=G	major_cov=26/21	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=26/21	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=26/21
RA	33	.	CP028101	880795	0	A	T	consensus_score=147.9	frequency=1	major_base=T	major_cov=24/21	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=24/21	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=24/21
RA	34	.	CP028101	880807	0	T	A	consensus_score=143.0	frequency=1	major_base=A	major_cov=22/21	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=22/21	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=22/21
RA	35	.	CP028101	880813	0	A	G	consensus_score=130.4	frequency=1	major_base=G	major_cov=20/21	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=20/21	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=20/21
RA	36	.	CP028101	901169	0	C	T	consensus_score=31.8	frequency=1	major_base=T	major_cov=8/11	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=8/11	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=8/11
RA	37	.	CP028101	1054222	0	G	.	bias_e_value=514024	bias_p_value=0.23578	consensus_reject=FREQUENCY_CUTOFF	consensus_score=161.6	fisher_strand_p_value=0.419292	frequency=4.343e-01	ks_quality_p_value=0.149055	major_base=G	major_cov=30/26	major_frequency=5.657e-01	minor_base=.	minor_cov=19/24	new_cov=19/24	polymorphism_frequency=4.343e-01	polymorphism_score=165.4	prediction=polymorphism	ref_cov=30/26	total_cov=49/51
RA	38	.	CP028101	1228379	0	T	.	bias_e_value=771570	bias_p_value=0.353915	consensus_reject=FREQUENCY_CUTOFF	consensus_score=86.4	fisher_strand_p_value=0.50962	frequency=3.500e-01	ks_quality_p_value=0.216839	major_base=T	major_cov=15/11	major_frequency=6.500e-01	minor_base=.	minor_cov=6/8	new_cov=6/8	polymorphism_frequency=3.500e-01	polymorphism_score=46.5	prediction=polymorphism	ref_cov=15/11	total_cov=21/19
RA	39	.	CP028101	1262493	0	C	T	consensus_score=74.2	frequency=1	major_base=T	major_cov=16/22	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=16/22	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=16/22
RA	40	.	CP028101	1262494	0	A	G	consensus_score=74.8	frequency=1	major_base=G	major_cov=16/22	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=16/22	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=16/22
RA	41	.	CP028101	1308184	0	A	G	bias_e_value=4.70387e-06	bias_p_value=2.15764e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=217.5	fisher_strand_p_value=6.89213e-14	frequency=2.685e-01	ks_quality_p_value=1	major_base=A	major_cov=19/60	major_frequency=7.315e-01	minor_base=G	minor_cov=29/0	new_cov=29/0	polymorphism_frequency=2.685e-01	polymorphism_score=18.1	prediction=polymorphism	ref_cov=19/60	total_cov=53/60
RA	42	.	CP028101	1308193	0	A	T	bias_e_value=0.445137	bias_p_value=2.04182e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=242.1	fisher_strand_p_value=1.05423e-08	frequency=2.000e-01	ks_quality_p_value=1	major_base=A	major_cov=29/55	major_frequency=8.000e-01	minor_base=T	minor_cov=21/0	new_cov=21/0	polymorphism_frequency=2.000e-01	polymorphism_score=10.9	prediction=polymorphism	ref_cov=29/55	total_cov=50/55
RA	43	.	CP028101	1308201	0	C	T	bias_e_value=9.06907e-08	bias_p_value=4.15993e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=212.8	fisher_strand_p_value=1.17589e-15	frequency=3.077e-01	ks_quality_p_value=1	major_base=C	major_cov=15/57	major_frequency=6.923e-01	minor_base=T	minor_cov=32/0	new_cov=32/0	polymorphism_frequency=3.077e-01	polymorphism_score=18.5	prediction=polymorphism	ref_cov=15/57	total_cov=48/57
RA	44	.	CP028101	1530400	1	.	C	bias_e_value=1845000	bias_p_value=0.846289	consensus_reject=FREQUENCY_CUTOFF	consensus_score=39.6	fisher_strand_p_value=1	frequency=4.545e-01	ks_quality_p_value=0.499589	major_base=.	major_cov=10/8	major_frequency=5.455e-01	minor_base=C	minor_cov=8/7	new_cov=8/7	polymorphism_frequency=4.545e-01	polymorphism_score=73.7	prediction=polymorphism	ref_cov=10/8	total_cov=18/15
RA	45	.	CP028101	1828290	0	C	T	bias_e_value=29344.9	bias_p_value=0.0134603	consensus_reject=FREQUENCY_CUTOFF	consensus_score=262.8	fisher_strand_p_value=1	frequency=2.727e-01	ks_quality_p_value=0.00184509	major_base=C	major_cov=57/55	major_frequency=7.273e-01	minor_base=T	minor_cov=22/20	new_cov=22/20	polymorphism_frequency=2.727e-01	polymorphism_score=127.0	prediction=polymorphism	ref_cov=57/55	total_cov=79/75
RA	46	.	CP028101	2048973	0	G	T	bias_e_value=0.00181992	bias_p_value=8.34788e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=147.3	fisher_strand_p_value=3.32217e-11	frequency=3.158e-01	ks_quality_p_value=1	major_base=G	major_cov=12/40	major_frequency=6.842e-01	minor_base=T	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=3.158e-01	polymorphism_score=23.7	prediction=polymorphism	ref_cov=12/40	total_cov=36/40
RA	47	.	CP028101	2117251	0	T	G	bias_e_value=4.14387e-12	bias_p_value=1.90077e-18	consensus_reject=FREQUENCY_CUTOFF	consensus_score=692.0	fisher_strand_p_value=4.1661e-20	frequency=2.143e-01	ks_quality_p_value=1	major_base=T	major_cov=89/131	major_frequency=7.857e-01	minor_base=G	minor_cov=60/0	new_cov=60/0	polymorphism_frequency=2.143e-01	polymorphism_score=32.6	prediction=polymorphism	ref_cov=89/131	total_cov=149/132
JC	1	.	CP028101	1	1	CP028101	2180101	-1	0	alignment_overlap=0	coverage_minus=57	coverage_plus=69	flanking_left=251	flanking_right=251	frequency=1	junction_possible_overlap_registers=221	key=CP028101__1__1__CP028101__2180101__-1__0____251__251__0__0	max_left=245	max_left_minus=214	max_left_plus=245	max_min_left=124	max_min_left_minus=118	max_min_left_plus=124	max_min_right=122	max_min_right_minus=120	max_min_right_plus=122	max_pos_hash_score=442	max_right=250	max_right_minus=248	max_right_plus=250	neg_log10_pos_hash_p_value=0.4	new_junction_coverage=0.93	new_junction_read_count=130	polymorphism_frequency=1.000e+00	pos_hash_score=63	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=221	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=221	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=126
JC	2	.	CP028101	14507	-1	CP028101	14845	-1	0	alignment_overlap=10	coverage_minus=2	coverage_plus=2	flanking_left=251	flanking_right=251	frequency=NA	junction_possible_overlap_registers=211	key=CP028101__14507__-1__CP028101__14855__-1__10____251__251__1__1	max_left=144	max_left_minus=144	max_left_plus=126	max_min_left=66	max_min_left_minus=66	max_min_left_plus=66	max_min_right=115	max_min_right_minus=96	max_min_right_plus=115	max_pos_hash_score=422	max_right=115	max_right_minus=96	max_right_plus=115	neg_log10_pos_hash_p_value=3.6	new_junction_coverage=0.03	new_junction_read_count=4	polymorphism_frequency=NA	pos_hash_score=4	prediction=unknown	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=10	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=4
JC	3	.	CP028101	14634	1	CP028101	15120	1	0	alignment_overlap=5	coverage_minus=3	coverage_plus=3	flanking_left=251	flanking_right=251	frequency=NA	junction_possible_overlap_registers=216	key=CP028101__14634__1__CP028101__15115__1__5____251__251__1__1	max_left=112	max_left_minus=112	max_left_plus=66	max_min_left=112	max_min_left_minus=112	max_min_left_plus=66	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=432	max_right=221	max_right_minus=174	max_right_plus=221	neg_log10_pos_hash_p_value=3.2	new_junction_coverage=0.04	new_junction_read_count=6	polymorphism_frequency=NA	pos_hash_score=6	prediction=unknown	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=5	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=6
JC	4	.	CP028101	134236	-1	CP028101	134652	-1	0	alignment_overlap=11	coverage_minus=2	coverage_plus=1	flanking_left=251	flanking_right=251	frequency=1.212e-02	junction_possible_overlap_registers=210	key=CP028101__134236__-1__CP028101__134663__-1__11____251__251__0__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=58	max_min_left_minus=58	max_min_left_plus=0	max_min_right=65	max_min_right_minus=65	max_min_right_plus=65	max_pos_hash_score=420	max_right=182	max_right_minus=182	max_right_plus=65	neg_log10_pos_hash_p_value=3.8	new_junction_coverage=0.02	new_junction_read_count=3	polymorphism_frequency=1.212e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.57	side_1_overlap=11	side_1_possible_overlap_registers=221	side_1_read_count=220	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=2.10	side_2_overlap=0	side_2_possible_overlap_registers=210	side_2_read_count=280	side_2_redundant=0	total_non_overlap_reads=3
JC	5	.	CP028101	137707	1	CP028101	137890	1	0	alignment_overlap=6	coverage_minus=1	coverage_plus=2	flanking_left=251	flanking_right=251	frequency=1.144e-02	junction_possible_overlap_registers=215	key=CP028101__137707__1__CP028101__137884__1__6____251__251__0__0	max_left=129	max_left_minus=46	max_left_plus=129	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=115	max_min_right_minus=0	max_min_right_plus=115	max_pos_hash_score=430	max_right=169	max_right_minus=169	max_right_plus=169	neg_log10_pos_hash_p_value=3.9	new_junction_coverage=0.03	new_junction_read_count=4	polymorphism_frequency=1.144e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=2.46	side_1_overlap=6	side_1_possible_overlap_registers=221	side_1_read_count=346	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=2.60	side_2_overlap=0	side_2_possible_overlap_registers=215	side_2_read_count=355	side_2_redundant=0	total_non_overlap_reads=3
JC	6	.	CP028101	332833	-1	CP028101	332842	-1	0	alignment_overlap=8	coverage_minus=16	coverage_plus=12	flanking_left=251	flanking_right=251	frequency=NA	junction_possible_overlap_registers=213	key=CP028101__332833__-1__CP028101__332850__-1__8____251__251__1__1	max_left=160	max_left_minus=160	max_left_plus=59	max_min_left=108	max_min_left_minus=108	max_min_left_plus=59	max_min_right=81	max_min_right_minus=81	max_min_right_plus=0	max_pos_hash_score=426	max_right=233	max_right_minus=230	max_right_plus=233	neg_log10_pos_hash_p_value=1.7	new_junction_coverage=0.21	new_junction_read_count=28	polymorphism_frequency=NA	pos_hash_score=20	prediction=unknown	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=8	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=28
JC	7	.	CP028101	477450	1	CP028101	477649	1	0	alignment_overlap=8	coverage_minus=2	coverage_plus=1	flanking_left=251	flanking_right=251	frequency=1.530e-02	junction_possible_overlap_registers=213	key=CP028101__477450__1__CP028101__477641__1__8____251__251__0__0	max_left=184	max_left_minus=184	max_left_plus=80	max_min_left=80	max_min_left_minus=0	max_min_left_plus=80	max_min_right=79	max_min_right_minus=79	max_min_right_plus=0	max_pos_hash_score=426	max_right=162	max_right_minus=79	max_right_plus=162	neg_log10_pos_hash_p_value=3.9	new_junction_coverage=0.02	new_junction_read_count=3	polymorphism_frequency=1.530e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.55	side_1_overlap=8	side_1_possible_overlap_registers=221	side_1_read_count=217	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.31	side_2_overlap=0	side_2_possible_overlap_registers=213	side_2_read_count=177	side_2_redundant=0	total_non_overlap_reads=3
JC	8	.	CP028101	493674	-1	CP028101	493722	1	-54	alignment_overlap=-54	coverage_minus=63	coverage_plus=76	flanking_left=251	flanking_right=251	frequency=NA	junction_possible_overlap_registers=167	key=CP028101__493674__-1__CP028101__493722__1__-54__GTTCAAGGAACAACAGCCACTCCAGAAGCAAGTGAAAATAAATAGGGGGTCGAG__251__251__1__1	max_left=196	max_left_minus=192	max_left_plus=196	max_min_left=98	max_min_left_minus=89	max_min_left_plus=98	max_min_right=96	max_min_right_minus=93	max_min_right_plus=96	max_pos_hash_score=334	max_right=187	max_right_minus=186	max_right_plus=187	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.36	new_junction_read_count=144	polymorphism_frequency=NA	pos_hash_score=71	prediction=unknown	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=139	unique_read_sequence=GTTCAAGGAACAACAGCCACTCCAGAAGCAAGTGAAAATAAATAGGGGGTCGAG
JC	9	.	CP028101	673858	1	CP028101	674067	1	0	alignment_overlap=9	coverage_minus=2	coverage_plus=1	flanking_left=251	flanking_right=251	frequency=2.247e-02	junction_possible_overlap_registers=212	key=CP028101__673858__1__CP028101__674058__1__9____251__251__0__0	max_left=170	max_left_minus=170	max_left_plus=101	max_min_left=101	max_min_left_minus=0	max_min_left_plus=101	max_min_right=77	max_min_right_minus=77	max_min_right_plus=0	max_pos_hash_score=424	max_right=141	max_right_minus=77	max_right_plus=141	neg_log10_pos_hash_p_value=3.9	new_junction_coverage=0.02	new_junction_read_count=3	polymorphism_frequency=2.247e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.04	side_1_overlap=9	side_1_possible_overlap_registers=221	side_1_read_count=146	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.90	side_2_overlap=0	side_2_possible_overlap_registers=212	side_2_read_count=121	side_2_redundant=0	total_non_overlap_reads=3
JC	10	.	CP028101	900717	1	CP028101	900717	-1	-10	alignment_overlap=-10	coverage_minus=55	coverage_plus=64	flanking_left=251	flanking_right=251	frequency=NA	junction_possible_overlap_registers=211	key=CP028101__900717__1__CP028101__900717__-1__-10__GATAAAGTGG__251__251__1__1	max_left=240	max_left_minus=240	max_left_plus=236	max_min_left=120	max_min_left_minus=118	max_min_left_plus=120	max_min_right=113	max_min_right_minus=107	max_min_right_plus=113	max_pos_hash_score=422	max_right=238	max_right_minus=238	max_right_plus=233	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=0.94	new_junction_read_count=126	polymorphism_frequency=NA	pos_hash_score=79	prediction=unknown	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=119	unique_read_sequence=GATAAAGTGG
JC	11	.	CP028101	1002075	1	CP028101	1002413	1	0	alignment_overlap=10	coverage_minus=2	coverage_plus=2	flanking_left=251	flanking_right=251	frequency=1	junction_possible_overlap_registers=211	key=CP028101__1002065__1__CP028101__1002413__1__10____251__251__1__0	max_left=115	max_left_minus=115	max_left_plus=96	max_min_left=115	max_min_left_minus=115	max_min_left_plus=96	max_min_right=66	max_min_right_minus=66	max_min_right_plus=66	max_pos_hash_score=422	max_right=144	max_right_minus=126	max_right_plus=144	neg_log10_pos_hash_p_value=3.6	new_junction_coverage=0.03	new_junction_read_count=4	polymorphism_frequency=1.000e+00	pos_hash_score=4	prediction=consensus	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=10	side_2_possible_overlap_registers=221	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=4
JC	12	.	CP028101	1012873	1	CP028101	1012900	-1	0	alignment_overlap=2	coverage_minus=19	coverage_plus=18	flanking_left=251	flanking_right=251	frequency=2.964e-01	junction_possible_overlap_registers=219	key=CP028101__1012873__1__CP028101__1012902__-1__2____251__251__0__0	max_left=244	max_left_minus=244	max_left_plus=189	max_min_left=109	max_min_left_minus=105	max_min_left_plus=109	max_min_right=111	max_min_right_minus=84	max_min_right_plus=111	max_pos_hash_score=438	max_right=238	max_right_minus=197	max_right_plus=238	neg_log10_pos_hash_p_value=1.1	new_junction_coverage=0.28	new_junction_read_count=39	polymorphism_frequency=2.964e-01	pos_hash_score=34	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.64	side_1_overlap=2	side_1_possible_overlap_registers=221	side_1_read_count=90	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.69	side_2_overlap=0	side_2_possible_overlap_registers=219	side_2_read_count=96	side_2_redundant=0	total_non_overlap_reads=37
JC	13	.	CP028101	1017553	-1	CP028101	1017608	1	0	alignment_overlap=17	coverage_minus=6	coverage_plus=3	flanking_left=251	flanking_right=251	frequency=7.180e-02	junction_possible_overlap_registers=204	key=CP028101__1017553__-1__CP028101__1017591__1__17____251__251__0__0	max_left=193	max_left_minus=193	max_left_plus=130	max_min_left=76	max_min_left_minus=76	max_min_left_plus=1	max_min_right=106	max_min_right_minus=106	max_min_right_plus=104	max_pos_hash_score=408	max_right=233	max_right_minus=158	max_right_plus=233	neg_log10_pos_hash_p_value=2.9	new_junction_coverage=0.08	new_junction_read_count=10	polymorphism_frequency=7.180e-02	pos_hash_score=7	prediction=polymorphism	reject=FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.97	side_1_overlap=17	side_1_possible_overlap_registers=221	side_1_read_count=136	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.03	side_2_overlap=0	side_2_possible_overlap_registers=204	side_2_read_count=133	side_2_redundant=0	total_non_overlap_reads=9
JC	14	.	CP028101	1018685	1	CP028101	1018757	-1	0	alignment_overlap=2	coverage_minus=6	coverage_plus=12	flanking_left=251	flanking_right=251	frequency=1.673e-01	junction_possible_overlap_registers=219	key=CP028101__1018685__1__CP028101__1018759__-1__2____251__251__0__0	max_left=238	max_left_minus=238	max_left_plus=198	max_min_left=119	max_min_left_minus=103	max_min_left_plus=119	max_min_right=97	max_min_right_minus=93	max_min_right_plus=97	max_pos_hash_score=438	max_right=236	max_right_minus=206	max_right_plus=236	neg_log10_pos_hash_p_value=2.0	new_junction_coverage=0.14	new_junction_read_count=19	polymorphism_frequency=1.673e-01	pos_hash_score=16	prediction=polymorphism	reject=FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.68	side_1_overlap=2	side_1_possible_overlap_registers=221	side_1_read_count=95	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.68	side_2_overlap=0	side_2_possible_overlap_registers=219	side_2_read_count=95	side_2_redundant=0	total_non_overlap_reads=18
JC	15	.	CP028101	1378569	-1	CP028101	1378689	-1	0	alignment_overlap=14	coverage_minus=2	coverage_plus=2	flanking_left=251	flanking_right=251	frequency=2.736e-02	junction_possible_overlap_registers=207	key=CP028101__1378569__-1__CP028101__1378703__-1__14____251__251__0__0	max_left=131	max_left_minus=131	max_left_plus=131	max_min_left=53	max_min_left_minus=53	max_min_left_plus=53	max_min_right=91	max_min_right_minus=91	max_min_right_plus=91	max_pos_hash_score=414	max_right=118	max_right_minus=118	max_right_plus=118	neg_log10_pos_hash_p_value=3.6	new_junction_coverage=0.03	new_junction_read_count=4	polymorphism_frequency=2.736e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.20	side_1_overlap=14	side_1_possible_overlap_registers=221	side_1_read_count=168	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.97	side_2_overlap=0	side_2_possible_overlap_registers=207	side_2_read_count=127	side_2_redundant=0	total_non_overlap_reads=4
JC	16	.	CP028101	1538202	-1	CP028101	1539472	-1	0	alignment_overlap=9	coverage_minus=2	coverage_plus=2	flanking_left=251	flanking_right=251	frequency=6.758e-02	junction_possible_overlap_registers=212	key=CP028101__1538202__-1__CP028101__1539481__-1__9____251__251__0__0	max_left=143	max_left_minus=143	max_left_plus=133	max_min_left=86	max_min_left_minus=0	max_min_left_plus=86	max_min_right=99	max_min_right_minus=99	max_min_right_plus=93	max_pos_hash_score=424	max_right=155	max_right_minus=99	max_right_plus=155	neg_log10_pos_hash_p_value=3.6	new_junction_coverage=0.03	new_junction_read_count=4	polymorphism_frequency=6.758e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.28	side_1_overlap=9	side_1_possible_overlap_registers=221	side_1_read_count=40	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.53	side_2_overlap=0	side_2_possible_overlap_registers=212	side_2_read_count=72	side_2_redundant=0	total_non_overlap_reads=4
JC	17	.	CP028101	1598724	-1	CP028101	1598877	-1	0	alignment_overlap=9	coverage_minus=1	coverage_plus=2	flanking_left=251	flanking_right=251	frequency=1.691e-02	junction_possible_overlap_registers=212	key=CP028101__1598724__-1__CP028101__1598886__-1__9____251__251__0__0	max_left=121	max_left_minus=100	max_left_plus=121	max_min_left=100	max_min_left_minus=100	max_min_left_plus=97	max_min_right=121	max_min_right_minus=0	max_min_right_plus=121	max_pos_hash_score=424	max_right=145	max_right_minus=142	max_right_plus=145	neg_log10_pos_hash_p_value=3.9	new_junction_coverage=0.02	new_junction_read_count=3	polymorphism_frequency=1.691e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.43	side_1_overlap=9	side_1_possible_overlap_registers=221	side_1_read_count=201	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.16	side_2_overlap=0	side_2_possible_overlap_registers=212	side_2_read_count=156	side_2_redundant=0	total_non_overlap_reads=3
JC	18	.	CP028101	1628697	-1	CP028101	1628907	-1	0	alignment_overlap=4	coverage_minus=3	coverage_plus=3	flanking_left=251	flanking_right=251	frequency=7.244e-02	junction_possible_overlap_registers=217	key=CP028101__1628697__-1__CP028101__1628911__-1__4____251__251__0__0	max_left=169	max_left_minus=169	max_left_plus=169	max_min_left=110	max_min_left_minus=0	max_min_left_plus=110	max_min_right=78	max_min_right_minus=78	max_min_right_plus=53	max_pos_hash_score=434	max_right=170	max_right_minus=78	max_right_plus=170	neg_log10_pos_hash_p_value=3.6	new_junction_coverage=0.04	new_junction_read_count=6	polymorphism_frequency=7.244e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.92	side_1_overlap=4	side_1_possible_overlap_registers=221	side_1_read_count=129	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.20	side_2_overlap=0	side_2_possible_overlap_registers=217	side_2_read_count=27	side_2_redundant=0	total_non_overlap_reads=6
JC	19	.	CP028101	1735536	-1	CP028101	1735631	-1	0	alignment_overlap=7	coverage_minus=2	coverage_plus=2	flanking_left=251	flanking_right=251	frequency=4.759e-02	junction_possible_overlap_registers=214	key=CP028101__1735536__-1__CP028101__1735638__-1__7____251__251__0__0	max_left=77	max_left_minus=77	max_left_plus=77	max_min_left=77	max_min_left_minus=77	max_min_left_plus=77	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=428	max_right=96	max_right_minus=96	max_right_plus=96	neg_log10_pos_hash_p_value=3.9	new_junction_coverage=0.03	new_junction_read_count=4	polymorphism_frequency=4.759e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.66	side_1_overlap=7	side_1_possible_overlap_registers=221	side_1_read_count=92	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.52	side_2_overlap=0	side_2_possible_overlap_registers=214	side_2_read_count=71	side_2_redundant=0	total_non_overlap_reads=4
JC	20	.	CP028101	2060542	1	CP028101	2060554	-1	0	alignment_overlap=1	coverage_minus=8	coverage_plus=8	flanking_left=251	flanking_right=251	frequency=5.967e-02	junction_possible_overlap_registers=220	key=CP028101__2060542__1__CP028101__2060555__-1__1____251__251__0__0	max_left=216	max_left_minus=216	max_left_plus=199	max_min_left=116	max_min_left_minus=116	max_min_left_plus=115	max_min_right=98	max_min_right_minus=85	max_min_right_plus=98	max_pos_hash_score=440	max_right=164	max_right_minus=164	max_right_plus=155	neg_log10_pos_hash_p_value=2.4	new_junction_coverage=0.12	new_junction_read_count=17	polymorphism_frequency=5.967e-02	pos_hash_score=12	prediction=polymorphism	reject=FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.87	side_1_overlap=1	side_1_possible_overlap_registers=221	side_1_read_count=263	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.96	side_2_overlap=0	side_2_possible_overlap_registers=220	side_2_read_count=274	side_2_redundant=0	total_non_overlap_reads=16
UN	48	.	CP028101	14436	14436
UN	49	.	CP028101	14438	14438
UN	50	.	CP028101	14441	14441
UN	51	.	CP028101	14443	15674
UN	52	.	CP028101	172843	173951
UN	53	.	CP028101	298899	304953
UN	54	.	CP028101	304955	304955
UN	55	.	CP028101	305486	305486
UN	56	.	CP028101	305489	306731
UN	57	.	CP028101	332308	336738
UN	58	.	CP028101	424433	424433
UN	59	.	CP028101	424450	424453
UN	60	.	CP028101	424459	424459
UN	61	.	CP028101	424461	424461
UN	62	.	CP028101	424486	424486
UN	63	.	CP028101	491743	493921
UN	64	.	CP028101	505792	505792
UN	65	.	CP028101	505797	508001
UN	66	.	CP028101	514506	514511
UN	67	.	CP028101	514513	514521
UN	68	.	CP028101	534830	536098
UN	69	.	CP028101	536765	539436
UN	70	.	CP028101	539441	539442
UN	71	.	CP028101	539448	539448
UN	72	.	CP028101	610784	611292
UN	73	.	CP028101	613707	617908
UN	74	.	CP028101	694008	694247
UN	75	.	CP028101	696599	696599
UN	76	.	CP028101	696601	697718
UN	77	.	CP028101	697727	697727
UN	78	.	CP028101	759758	760971
UN	79	.	CP028101	760973	760973
UN	80	.	CP028101	760975	760975
UN	81	.	CP028101	761717	767789
UN	82	.	CP028101	772018	772019
UN	83	.	CP028101	772021	773153
UN	84	.	CP028101	873426	875284
UN	85	.	CP028101	900634	901143
UN	86	.	CP028101	1001160	1002450
UN	87	.	CP028101	1040991	1042306
UN	88	.	CP028101	1079694	1084191
UN	89	.	CP028101	1138394	1138906
UN	90	.	CP028101	1166518	1167676
UN	91	.	CP028101	1167678	1167678
UN	92	.	CP028101	1192511	1193786
UN	93	.	CP028101	1193788	1193791
UN	94	.	CP028101	1261924	1262410
UN	95	.	CP028101	1262415	1262415
UN	96	.	CP028101	1450203	1451191
UN	97	.	CP028101	1509127	1509127
UN	98	.	CP028101	1509133	1510002
UN	99	.	CP028101	1999580	2000615
UN	100	.	CP028101	2000618	2000618
UN	101	.	CP028101	2000621	2000621
UN	102	.	CP028101	2015676	2016684
UN	103	.	CP028101	2016686	2016686
UN	104	.	CP028101	2051474	2055954
UN	105	.	CP028101	2100309	2100823
UN	106	.	CP028101	2117867	2118837
UN	107	.	CP028101	2124060	2124314