#=GENOME_DIFF 1.0 #=CREATED 15:55:17 23 May 2019 #=PROGRAM breseq 0.33.1 revision 8505477f25b3 #=COMMAND /usr/bin/breseq-0.33.1-Linux-x86_64/bin/breseq --consensus-frequency-cutoff=0.75 --require-match-fraction=0.95 -p -j 1 -o breseq_processes/36 -r /var/data/TCH1516_HM_ALE_referencePlusProkka_Jan2019.gbk /var/alemutpipe-outputs/good/SNFM_3_44_0_S2694_L006_R1_001.good.fq.gz /var/alemutpipe-outputs/good/SNFM_3_44_0_S2694_L006_R2_001.good.fq.gz #=REFSEQ /var/data/TCH1516_HM_ALE_referencePlusProkka_Jan2019.gbk #=READSEQ /var/alemutpipe-outputs/good/SNFM_3_44_0_S2694_L006_R1_001.good.fq.gz #=READSEQ /var/alemutpipe-outputs/good/SNFM_3_44_0_S2694_L006_R2_001.good.fq.gz #=CONVERTED-BASES 129861082 #=CONVERTED-READS 921266 #=INPUT-BASES 129861082 #=INPUT-READS 921266 #=MAPPED-BASES 127978746 #=MAPPED-READS 908299 SNP 1 65 CP000731 81 G frequency=1 INS 2 130 CP000731 6552 TCTCCAGGCACTTGTGCATATTCTGAAA frequency=1 DEL 3 66 CP000731 25663 1 frequency=1 SNP 4 67 USA300TCH1516_ALE 37589 T frequency=7.95578957e-02 SNP 5 68 USA300TCH1516_ALE 94164 A frequency=8.71319771e-02 SNP 6 69 USA300TCH1516_ALE 108148 G frequency=1.17556572e-01 SNP 7 70 USA300TCH1516_ALE 110651 T frequency=1.05979443e-01 SNP 8 71 USA300TCH1516_ALE 110660 A frequency=1.22707367e-01 SNP 9 72 USA300TCH1516_ALE 111512 G frequency=2.38242626e-01 SNP 10 73 USA300TCH1516_ALE 111516 A frequency=2.49879360e-01 SNP 11 74 USA300TCH1516_ALE 187439 T frequency=7.95636177e-02 SNP 12 75 USA300TCH1516_ALE 189365 G frequency=1.66663647e-01 SNP 13 76 USA300TCH1516_ALE 264793 C frequency=8.16788673e-02 SNP 14 77 USA300TCH1516_ALE 265956 C frequency=1.14360809e-01 SNP 15 78 USA300TCH1516_ALE 387871 T frequency=8.32710266e-02 SNP 16 79 USA300TCH1516_ALE 414995 C frequency=7.02443123e-02 SNP 17 80 USA300TCH1516_ALE 494590 G frequency=9.30933952e-02 SNP 18 81 USA300TCH1516_ALE 512643 G frequency=4.82234478e-01 DEL 19 82 USA300TCH1516_ALE 591934 1 frequency=5.26204109e-02 SNP 20 83 USA300TCH1516_ALE 622019 C frequency=9.72237587e-02 SNP 21 84 USA300TCH1516_ALE 866495 A frequency=1.23833179e-01 SNP 22 85 USA300TCH1516_ALE 915857 T frequency=9.00549889e-02 SNP 23 86 USA300TCH1516_ALE 966439 G frequency=7.14807510e-02 SNP 24 87 USA300TCH1516_ALE 984788 T frequency=9.99946594e-02 SNP 25 88 USA300TCH1516_ALE 989442 A frequency=9.98229980e-02 SNP 26 89 USA300TCH1516_ALE 995747 T frequency=9.86967087e-02 SNP 27 90 USA300TCH1516_ALE 1091403 C frequency=1.19783401e-01 SNP 28 91 USA300TCH1516_ALE 1181141 C frequency=7.93428421e-02 SNP 29 92 USA300TCH1516_ALE 1202470 A frequency=9.98950005e-02 SNP 30 93 USA300TCH1516_ALE 1276099 A frequency=8.52351189e-02 SNP 31 94 USA300TCH1516_ALE 1291644 A frequency=1.26275063e-01 SNP 32 95 USA300TCH1516_ALE 1414715 C frequency=1.51968956e-01 SNP 33 96 USA300TCH1516_ALE 1416458 T frequency=1 SNP 34 97 USA300TCH1516_ALE 1513930 T frequency=1 SNP 35 98 USA300TCH1516_ALE 1540760 G frequency=1.03408337e-01 SNP 36 99 USA300TCH1516_ALE 1646189 C frequency=1 SNP 37 100 USA300TCH1516_ALE 1672327 G frequency=1.63212776e-01 SNP 38 101 USA300TCH1516_ALE 1732905 A frequency=1.08123302e-01 SNP 39 102 USA300TCH1516_ALE 1776059 G frequency=6.82277679e-02 SNP 40 103 USA300TCH1516_ALE 1797152 A frequency=1.83512688e-01 SNP 41 104 USA300TCH1516_ALE 1842707 C frequency=6.89368248e-02 SNP 42 105 USA300TCH1516_ALE 1980512 T frequency=6.51693344e-02 SNP 43 106 USA300TCH1516_ALE 2010363 T frequency=1 SNP 44 107 USA300TCH1516_ALE 2018582 A frequency=9.75508690e-02 SNP 45 108 USA300TCH1516_ALE 2028124 A frequency=3.41590881e-01 SNP 46 109 USA300TCH1516_ALE 2057798 A frequency=5.47676086e-02 SNP 47 110 USA300TCH1516_ALE 2094261 G frequency=1.42829895e-01 SNP 48 111 USA300TCH1516_ALE 2101143 G frequency=5.54571152e-02 SNP 49 112 USA300TCH1516_ALE 2128065 G frequency=1.81952000e-01 SNP 50 113 USA300TCH1516_ALE 2279705 A frequency=1 SNP 51 114 USA300TCH1516_ALE 2358670 C frequency=1.00135326e-01 SNP 52 115 USA300TCH1516_ALE 2372751 T frequency=2.30885983e-01 SNP 53 116 USA300TCH1516_ALE 2373531 T frequency=1.35804653e-01 SNP 54 117 USA300TCH1516_ALE 2373714 T frequency=3.32982540e-01 SNP 55 118 USA300TCH1516_ALE 2405833 G frequency=9.29470062e-02 SNP 56 119 USA300TCH1516_ALE 2425673 G frequency=1.15665436e-01 SNP 57 120 USA300TCH1516_ALE 2451070 C frequency=9.75403786e-02 SNP 58 121 USA300TCH1516_ALE 2462758 A frequency=2.49992371e-01 SNP 59 122 USA300TCH1516_ALE 2532298 T frequency=1 SNP 60 123 USA300TCH1516_ALE 2532665 T frequency=1.02644444e-01 SNP 61 124 USA300TCH1516_ALE 2568885 A frequency=9.30323601e-02 SNP 62 125 USA300TCH1516_ALE 2615078 G frequency=1.70495033e-01 SNP 63 126 USA300TCH1516_ALE 2638727 T frequency=8.70294571e-02 SNP 64 127 USA300TCH1516_ALE 2656802 T frequency=6.41651154e-02 RA 65 . CP000731 81 0 N G consensus_score=385.2 frequency=1 major_base=G major_cov=53/47 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=53/47 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=53/47 RA 66 . CP000731 25663 0 A . bias_e_value=2903080 bias_p_value=1 consensus_score=415.4 fisher_strand_p_value=1 frequency=1 ks_quality_p_value=1 major_base=. major_cov=43/43 major_frequency=9.88532066e-01 minor_base=A minor_cov=0/1 new_cov=43/43 polymorphism_frequency=9.88532066e-01 polymorphism_reject=SCORE_CUTOFF,FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE,INDEL_HOMOPOLYMER polymorphism_score=-3.4 prediction=consensus ref_cov=0/1 total_cov=43/44 RA 67 . USA300TCH1516_ALE 37589 0 G T bias_e_value=2903080 bias_p_value=1 consensus_score=165.9 fisher_strand_p_value=1 frequency=7.95578957e-02 ks_quality_p_value=1 major_base=G major_cov=18/24 major_frequency=9.20442104e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=7.95578957e-02 polymorphism_score=2.1 prediction=polymorphism ref_cov=18/24 total_cov=20/26 RA 68 . USA300TCH1516_ALE 94164 0 G A bias_e_value=2903080 bias_p_value=1 consensus_score=133.7 fisher_strand_p_value=1 frequency=8.71319771e-02 ks_quality_p_value=1 major_base=G major_cov=18/21 major_frequency=9.12868023e-01 minor_base=A minor_cov=2/2 new_cov=2/2 polymorphism_frequency=8.71319771e-02 polymorphism_score=2.4 prediction=polymorphism ref_cov=18/21 total_cov=20/23 RA 69 . USA300TCH1516_ALE 108148 0 A G bias_e_value=2593670 bias_p_value=0.893419 consensus_score=90.7 fisher_strand_p_value=0.579934 frequency=1.17556572e-01 ks_quality_p_value=0.992188 major_base=A major_cov=9/21 major_frequency=8.82443428e-01 minor_base=G minor_cov=2/2 new_cov=2/2 polymorphism_frequency=1.17556572e-01 polymorphism_score=5.0 prediction=polymorphism ref_cov=9/21 total_cov=11/23 RA 70 . USA300TCH1516_ALE 110651 0 C T bias_e_value=2241120 bias_p_value=0.771981 consensus_score=168.5 fisher_strand_p_value=0.406014 frequency=1.05979443e-01 ks_quality_p_value=1 major_base=C major_cov=22/27 major_frequency=8.94020557e-01 minor_base=T minor_cov=4/2 new_cov=4/2 polymorphism_frequency=1.05979443e-01 polymorphism_score=7.8 prediction=polymorphism ref_cov=22/27 total_cov=26/29 RA 71 . USA300TCH1516_ALE 110660 0 T A bias_e_value=2713020 bias_p_value=0.934532 consensus_score=175.3 fisher_strand_p_value=0.69057 frequency=1.22707367e-01 ks_quality_p_value=0.956753 major_base=T major_cov=22/28 major_frequency=8.77292633e-01 minor_base=A minor_cov=4/3 new_cov=4/3 polymorphism_frequency=1.22707367e-01 polymorphism_score=16.0 prediction=polymorphism ref_cov=22/28 total_cov=26/31 RA 72 . USA300TCH1516_ALE 111512 0 A G bias_e_value=2808690 bias_p_value=0.967487 consensus_score=120.7 fisher_strand_p_value=0.763621 frequency=2.38242626e-01 ks_quality_p_value=0.990128 major_base=A major_cov=20/28 major_frequency=7.61757374e-01 minor_base=G minor_cov=5/10 new_cov=5/10 polymorphism_frequency=2.38242626e-01 polymorphism_score=37.9 prediction=polymorphism ref_cov=20/28 total_cov=25/38 RA 73 . USA300TCH1516_ALE 111516 0 C A bias_e_value=2902880 bias_p_value=0.99993 consensus_score=141.4 fisher_strand_p_value=1 frequency=2.49879360e-01 ks_quality_p_value=0.988166 major_base=C major_cov=16/26 major_frequency=7.50120640e-01 minor_base=A minor_cov=5/9 new_cov=5/9 polymorphism_frequency=2.49879360e-01 polymorphism_score=34.8 prediction=polymorphism ref_cov=16/26 total_cov=21/35 RA 74 . USA300TCH1516_ALE 187439 0 G T bias_e_value=2903080 bias_p_value=1 consensus_score=202.2 fisher_strand_p_value=1 frequency=7.95636177e-02 ks_quality_p_value=1 major_base=G major_cov=24/28 major_frequency=9.20436382e-01 minor_base=T minor_cov=2/3 new_cov=2/3 polymorphism_frequency=7.95636177e-02 polymorphism_score=2.9 prediction=polymorphism ref_cov=24/28 total_cov=26/31 RA 75 . USA300TCH1516_ALE 189365 0 A G bias_e_value=2902900 bias_p_value=0.999939 consensus_score=84.5 fisher_strand_p_value=1 frequency=1.66663647e-01 ks_quality_p_value=0.98895 major_base=A major_cov=13/17 major_frequency=8.33336353e-01 minor_base=G minor_cov=3/3 new_cov=3/3 polymorphism_frequency=1.66663647e-01 polymorphism_score=10.7 prediction=polymorphism ref_cov=13/17 total_cov=16/20 RA 76 . USA300TCH1516_ALE 264793 0 T C bias_e_value=2898370 bias_p_value=0.998379 consensus_score=138.0 fisher_strand_p_value=1 frequency=8.16788673e-02 ks_quality_p_value=0.943603 major_base=T major_cov=26/19 major_frequency=9.18321133e-01 minor_base=C minor_cov=2/2 new_cov=2/2 polymorphism_frequency=8.16788673e-02 polymorphism_score=4.3 prediction=polymorphism ref_cov=26/19 total_cov=28/21 RA 77 . USA300TCH1516_ALE 265956 0 T C bias_e_value=2302760 bias_p_value=0.793213 consensus_score=87.7 fisher_strand_p_value=0.617647 frequency=1.14360809e-01 ks_quality_p_value=0.696777 major_base=T major_cov=11/20 major_frequency=8.85639191e-01 minor_base=C minor_cov=2/2 new_cov=2/2 polymorphism_frequency=1.14360809e-01 polymorphism_score=5.6 prediction=polymorphism ref_cov=11/20 total_cov=13/22 RA 78 . USA300TCH1516_ALE 387871 0 G T bias_e_value=2890860 bias_p_value=0.99579 consensus_score=176.0 fisher_strand_p_value=1 frequency=8.32710266e-02 ks_quality_p_value=0.909649 major_base=G major_cov=23/21 major_frequency=9.16728973e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=8.32710266e-02 polymorphism_score=5.2 prediction=polymorphism ref_cov=23/21 total_cov=25/23 RA 79 . USA300TCH1516_ALE 414995 0 T C bias_e_value=2624300 bias_p_value=0.90397 consensus_score=169.9 fisher_strand_p_value=1 frequency=7.02443123e-02 ks_quality_p_value=0.595095 major_base=T major_cov=29/24 major_frequency=9.29755688e-01 minor_base=C minor_cov=2/2 new_cov=2/2 polymorphism_frequency=7.02443123e-02 polymorphism_score=4.8 prediction=polymorphism ref_cov=29/24 total_cov=31/26 RA 80 . USA300TCH1516_ALE 494590 0 A G bias_e_value=2792410 bias_p_value=0.961877 consensus_score=125.1 fisher_strand_p_value=1 frequency=9.30933952e-02 ks_quality_p_value=0.736897 major_base=A major_cov=21/18 major_frequency=9.06906605e-01 minor_base=G minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.30933952e-02 polymorphism_score=5.4 prediction=polymorphism ref_cov=21/18 total_cov=23/20 RA 81 . USA300TCH1516_ALE 512643 0 A G bias_e_value=2865800 bias_p_value=0.987159 consensus_score=-2.6 fisher_strand_p_value=1 frequency=4.82234478e-01 ks_quality_p_value=0.844082 major_base=A major_cov=27/17 major_frequency=5.17765522e-01 minor_base=G minor_cov=25/16 new_cov=25/16 polymorphism_frequency=4.82234478e-01 polymorphism_score=130.4 prediction=polymorphism ref_cov=27/17 total_cov=52/33 RA 82 . USA300TCH1516_ALE 591934 0 A . bias_e_value=2649040 bias_p_value=0.912492 consensus_score=258.2 fisher_strand_p_value=0.645044 frequency=5.26204109e-02 ks_quality_p_value=0.948729 major_base=A major_cov=44/28 major_frequency=9.47379589e-01 minor_base=. minor_cov=2/2 new_cov=2/2 polymorphism_frequency=5.26204109e-02 polymorphism_score=7.7 prediction=polymorphism ref_cov=44/28 total_cov=46/30 RA 83 . USA300TCH1516_ALE 622019 0 T C bias_e_value=2902440 bias_p_value=0.999781 consensus_score=113.2 fisher_strand_p_value=1 frequency=9.72237587e-02 ks_quality_p_value=0.979127 major_base=T major_cov=22/15 major_frequency=9.02776241e-01 minor_base=C minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.72237587e-02 polymorphism_score=2.9 prediction=polymorphism ref_cov=22/15 total_cov=24/17 RA 84 . USA300TCH1516_ALE 866495 0 G A bias_e_value=2720410 bias_p_value=0.937078 consensus_score=138.0 fisher_strand_p_value=0.682985 frequency=1.23833179e-01 ks_quality_p_value=0.976472 major_base=G major_cov=25/17 major_frequency=8.76166821e-01 minor_base=A minor_cov=3/3 new_cov=3/3 polymorphism_frequency=1.23833179e-01 polymorphism_score=8.0 prediction=polymorphism ref_cov=25/17 total_cov=28/20 RA 85 . USA300TCH1516_ALE 915857 0 C T bias_e_value=2903050 bias_p_value=0.99999 consensus_score=135.2 fisher_strand_p_value=1 frequency=9.00549889e-02 ks_quality_p_value=0.995465 major_base=C major_cov=17/23 major_frequency=9.09945011e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.00549889e-02 polymorphism_score=3.2 prediction=polymorphism ref_cov=17/23 total_cov=19/25 RA 86 . USA300TCH1516_ALE 966439 0 A G bias_e_value=1682650 bias_p_value=0.579607 consensus_score=168.6 fisher_strand_p_value=0.641569 frequency=7.14807510e-02 ks_quality_p_value=0.370924 major_base=A major_cov=32/20 major_frequency=9.28519249e-01 minor_base=G minor_cov=2/2 new_cov=2/2 polymorphism_frequency=7.14807510e-02 polymorphism_score=4.9 prediction=polymorphism ref_cov=32/20 total_cov=34/22 RA 87 . USA300TCH1516_ALE 984788 0 C T bias_e_value=2478620 bias_p_value=0.853791 consensus_score=119.2 fisher_strand_p_value=1 frequency=9.99946594e-02 ks_quality_p_value=0.510573 major_base=C major_cov=15/21 major_frequency=9.00005341e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.99946594e-02 polymorphism_score=4.9 prediction=polymorphism ref_cov=15/21 total_cov=17/23 RA 88 . USA300TCH1516_ALE 989442 0 C A bias_e_value=2852210 bias_p_value=0.982477 consensus_score=128.2 fisher_strand_p_value=1 frequency=9.98229980e-02 ks_quality_p_value=0.818731 major_base=C major_cov=20/16 major_frequency=9.00177002e-01 minor_base=A minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.98229980e-02 polymorphism_score=3.5 prediction=polymorphism ref_cov=20/16 total_cov=22/18 RA 89 . USA300TCH1516_ALE 995747 0 C T bias_e_value=2877540 bias_p_value=0.991203 consensus_score=118.1 fisher_strand_p_value=1 frequency=9.86967087e-02 ks_quality_p_value=0.870325 major_base=C major_cov=14/22 major_frequency=9.01303291e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.86967087e-02 polymorphism_score=3.2 prediction=polymorphism ref_cov=14/22 total_cov=16/24 RA 90 . USA300TCH1516_ALE 1091403 0 T C bias_e_value=2902980 bias_p_value=0.999965 consensus_score=83.4 fisher_strand_p_value=1 frequency=1.19783401e-01 ks_quality_p_value=0.991675 major_base=T major_cov=18/11 major_frequency=8.80216599e-01 minor_base=C minor_cov=2/2 new_cov=2/2 polymorphism_frequency=1.19783401e-01 polymorphism_score=3.1 prediction=polymorphism ref_cov=18/11 total_cov=21/14 RA 91 . USA300TCH1516_ALE 1181141 0 T C bias_e_value=2646510 bias_p_value=0.911622 consensus_score=152.7 fisher_strand_p_value=0.612332 frequency=7.93428421e-02 ks_quality_p_value=0.996528 major_base=T major_cov=30/16 major_frequency=9.20657158e-01 minor_base=C minor_cov=2/2 new_cov=2/2 polymorphism_frequency=7.93428421e-02 polymorphism_score=2.3 prediction=polymorphism ref_cov=30/16 total_cov=32/18 RA 92 . USA300TCH1516_ALE 1202470 0 G A bias_e_value=2899570 bias_p_value=0.998791 consensus_score=123.7 fisher_strand_p_value=1 frequency=9.98950005e-02 ks_quality_p_value=0.951229 major_base=G major_cov=16/20 major_frequency=9.00105000e-01 minor_base=A minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.98950005e-02 polymorphism_score=4.7 prediction=polymorphism ref_cov=16/20 total_cov=18/22 RA 93 . USA300TCH1516_ALE 1276099 0 T A bias_e_value=2659530 bias_p_value=0.916105 consensus_score=145.4 fisher_strand_p_value=1 frequency=8.52351189e-02 ks_quality_p_value=0.619421 major_base=T major_cov=18/25 major_frequency=9.14764881e-01 minor_base=A minor_cov=2/2 new_cov=2/2 polymorphism_frequency=8.52351189e-02 polymorphism_score=7.0 prediction=polymorphism ref_cov=18/25 total_cov=20/27 RA 94 . USA300TCH1516_ALE 1291644 0 G A bias_e_value=2896690 bias_p_value=0.997798 consensus_score=109.8 fisher_strand_p_value=1 frequency=1.26275063e-01 ks_quality_p_value=0.934379 major_base=G major_cov=18/16 major_frequency=8.73724937e-01 minor_base=A minor_cov=3/2 new_cov=3/2 polymorphism_frequency=1.26275063e-01 polymorphism_score=6.0 prediction=polymorphism ref_cov=18/16 total_cov=21/19 RA 95 . USA300TCH1516_ALE 1414715 0 T C bias_e_value=2696330 bias_p_value=0.928784 consensus_score=96.0 fisher_strand_p_value=0.64717 frequency=1.51968956e-01 ks_quality_p_value=1 major_base=T major_cov=11/22 major_frequency=8.48031044e-01 minor_base=C minor_cov=3/3 new_cov=3/3 polymorphism_frequency=1.51968956e-01 polymorphism_score=10.6 prediction=polymorphism ref_cov=11/22 total_cov=14/25 RA 96 . USA300TCH1516_ALE 1416458 0 A T consensus_score=143.6 frequency=1 major_base=T major_cov=15/24 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=15/24 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=15/24 RA 97 . USA300TCH1516_ALE 1513930 0 A T consensus_score=84.2 frequency=1 major_base=T major_cov=4/19 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=4/19 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=4/19 RA 98 . USA300TCH1516_ALE 1540760 0 A G bias_e_value=2727450 bias_p_value=0.939502 consensus_score=165.3 fisher_strand_p_value=0.683764 frequency=1.03408337e-01 ks_quality_p_value=0.984211 major_base=A major_cov=31/21 major_frequency=8.96591663e-01 minor_base=G minor_cov=3/3 new_cov=3/3 polymorphism_frequency=1.03408337e-01 polymorphism_score=8.9 prediction=polymorphism ref_cov=31/21 total_cov=34/24 RA 99 . USA300TCH1516_ALE 1646189 0 G C consensus_score=107.7 frequency=1 major_base=C major_cov=15/13 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=15/13 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=15/13 RA 100 . USA300TCH1516_ALE 1672327 0 A G bias_e_value=2902750 bias_p_value=0.999885 consensus_score=58.0 fisher_strand_p_value=1 frequency=1.63212776e-01 ks_quality_p_value=0.984877 major_base=A major_cov=10/11 major_frequency=8.36787224e-01 minor_base=G minor_cov=2/2 new_cov=2/2 polymorphism_frequency=1.63212776e-01 polymorphism_score=5.3 prediction=polymorphism ref_cov=10/11 total_cov=12/14 RA 101 . USA300TCH1516_ALE 1732905 0 T A bias_e_value=2001880 bias_p_value=0.689572 consensus_score=111.6 fisher_strand_p_value=0.624589 frequency=1.08123302e-01 ks_quality_p_value=0.519338 major_base=T major_cov=21/12 major_frequency=8.91876698e-01 minor_base=A minor_cov=2/2 new_cov=2/2 polymorphism_frequency=1.08123302e-01 polymorphism_score=7.4 prediction=polymorphism ref_cov=21/12 total_cov=23/14 RA 102 . USA300TCH1516_ALE 1776059 0 A G bias_e_value=1346050 bias_p_value=0.463663 consensus_score=163.2 fisher_strand_p_value=1 frequency=6.82277679e-02 ks_quality_p_value=0.165758 major_base=A major_cov=25/30 major_frequency=9.31772232e-01 minor_base=G minor_cov=2/2 new_cov=2/2 polymorphism_frequency=6.82277679e-02 polymorphism_score=5.3 prediction=polymorphism ref_cov=25/30 total_cov=27/32 RA 103 . USA300TCH1516_ALE 1797152 0 G A bias_e_value=2503270 bias_p_value=0.862281 consensus_score=84.3 fisher_strand_p_value=0.692795 frequency=1.83512688e-01 ks_quality_p_value=0.75555 major_base=G major_cov=16/14 major_frequency=8.16487312e-01 minor_base=A minor_cov=3/4 new_cov=3/4 polymorphism_frequency=1.83512688e-01 polymorphism_score=12.1 prediction=polymorphism ref_cov=16/14 total_cov=19/18 RA 104 . USA300TCH1516_ALE 1842707 0 T C bias_e_value=2900720 bias_p_value=0.999187 consensus_score=184.8 fisher_strand_p_value=1 frequency=6.89368248e-02 ks_quality_p_value=0.959955 major_base=T major_cov=31/23 major_frequency=9.31063175e-01 minor_base=C minor_cov=2/2 new_cov=2/2 polymorphism_frequency=6.89368248e-02 polymorphism_score=5.0 prediction=polymorphism ref_cov=31/23 total_cov=33/25 RA 105 . USA300TCH1516_ALE 1980512 0 G T bias_e_value=2898460 bias_p_value=0.998408 consensus_score=215.2 fisher_strand_p_value=1 frequency=6.51693344e-02 ks_quality_p_value=0.944102 major_base=G major_cov=24/33 major_frequency=9.34830666e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=6.51693344e-02 polymorphism_score=3.3 prediction=polymorphism ref_cov=24/33 total_cov=26/35 RA 106 . USA300TCH1516_ALE 2010363 0 C T consensus_score=195.0 frequency=1 major_base=T major_cov=19/33 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=19/33 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=19/33 RA 107 . USA300TCH1516_ALE 2018582 0 T A bias_e_value=2702830 bias_p_value=0.931021 consensus_score=131.6 fisher_strand_p_value=1 frequency=9.75508690e-02 ks_quality_p_value=0.65236 major_base=T major_cov=15/22 major_frequency=9.02449131e-01 minor_base=A minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.75508690e-02 polymorphism_score=8.1 prediction=polymorphism ref_cov=15/22 total_cov=17/24 RA 108 . USA300TCH1516_ALE 2028124 0 G A bias_e_value=1856740 bias_p_value=0.639577 consensus_score=42.0 fisher_strand_p_value=0.282481 frequency=3.41590881e-01 ks_quality_p_value=1 major_base=G major_cov=8/15 major_frequency=6.58409119e-01 minor_base=A minor_cov=7/5 new_cov=7/5 polymorphism_frequency=3.41590881e-01 polymorphism_score=28.6 prediction=polymorphism ref_cov=8/15 total_cov=15/20 RA 109 . USA300TCH1516_ALE 2057798 0 C A bias_e_value=2691390 bias_p_value=0.92708 consensus_score=268.1 fisher_strand_p_value=0.644364 frequency=5.47676086e-02 ks_quality_p_value=0.99832 major_base=C major_cov=41/26 major_frequency=9.45232391e-01 minor_base=A minor_cov=2/2 new_cov=2/2 polymorphism_frequency=5.47676086e-02 polymorphism_score=2.5 prediction=polymorphism ref_cov=41/26 total_cov=43/28 RA 110 . USA300TCH1516_ALE 2094261 0 A G bias_e_value=2881570 bias_p_value=0.992589 consensus_score=105.2 fisher_strand_p_value=1 frequency=1.42829895e-01 ks_quality_p_value=0.880748 major_base=A major_cov=17/19 major_frequency=8.57170105e-01 minor_base=G minor_cov=3/3 new_cov=3/3 polymorphism_frequency=1.42829895e-01 polymorphism_score=11.5 prediction=polymorphism ref_cov=17/19 total_cov=20/22 RA 111 . USA300TCH1516_ALE 2101143 0 A G bias_e_value=2898250 bias_p_value=0.998336 consensus_score=237.8 fisher_strand_p_value=1 frequency=5.54571152e-02 ks_quality_p_value=0.942873 major_base=A major_cov=39/29 major_frequency=9.44542885e-01 minor_base=G minor_cov=2/2 new_cov=2/2 polymorphism_frequency=5.54571152e-02 polymorphism_score=3.9 prediction=polymorphism ref_cov=39/29 total_cov=41/31 RA 112 . USA300TCH1516_ALE 2128065 0 A G bias_e_value=2289480 bias_p_value=0.78864 consensus_score=95.5 fisher_strand_p_value=0.697141 frequency=1.81952000e-01 ks_quality_p_value=0.609602 major_base=A major_cov=22/14 major_frequency=8.18048000e-01 minor_base=G minor_cov=4/4 new_cov=4/4 polymorphism_frequency=1.81952000e-01 polymorphism_score=18.6 prediction=polymorphism ref_cov=22/14 total_cov=26/18 RA 113 . USA300TCH1516_ALE 2279705 0 G A consensus_score=205.4 frequency=1 major_base=A major_cov=36/20 major_frequency=1.00000000e+00 minor_base=C minor_cov=1/0 new_cov=36/20 polymorphism_frequency=1.00000000e+00 polymorphism_reject=SCORE_CUTOFF,FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=-6.5 prediction=consensus ref_cov=0/0 total_cov=37/20 RA 114 . USA300TCH1516_ALE 2358670 0 T C bias_e_value=2879460 bias_p_value=0.991863 consensus_score=171.0 fisher_strand_p_value=1 frequency=1.00135326e-01 ks_quality_p_value=0.875173 major_base=T major_cov=23/31 major_frequency=8.99864674e-01 minor_base=C minor_cov=3/3 new_cov=3/3 polymorphism_frequency=1.00135326e-01 polymorphism_score=11.2 prediction=polymorphism ref_cov=23/31 total_cov=26/34 RA 115 . USA300TCH1516_ALE 2372751 0 A T bias_e_value=2365100 bias_p_value=0.814688 consensus_score=154.6 fisher_strand_p_value=0.487764 frequency=2.30885983e-01 ks_quality_p_value=0.936467 major_base=A major_cov=37/13 major_frequency=7.69114017e-01 minor_base=T minor_cov=13/2 new_cov=13/2 polymorphism_frequency=2.30885983e-01 polymorphism_score=46.1 prediction=polymorphism ref_cov=37/13 total_cov=50/15 RA 116 . USA300TCH1516_ALE 2373531 0 G T bias_e_value=2367430 bias_p_value=0.81549 consensus_score=156.8 fisher_strand_p_value=0.68432 frequency=1.35804653e-01 ks_quality_p_value=0.668985 major_base=G major_cov=25/18 major_frequency=8.64195347e-01 minor_base=T minor_cov=3/4 new_cov=3/4 polymorphism_frequency=1.35804653e-01 polymorphism_score=12.1 prediction=polymorphism ref_cov=25/18 total_cov=28/22 RA 117 . USA300TCH1516_ALE 2373714 0 C T bias_e_value=1454640 bias_p_value=0.501067 consensus_score=53.9 fisher_strand_p_value=0.204732 frequency=3.32982540e-01 ks_quality_p_value=0.914947 major_base=C major_cov=11/19 major_frequency=6.67017460e-01 minor_base=T minor_cov=9/6 new_cov=9/6 polymorphism_frequency=3.32982540e-01 polymorphism_score=35.6 prediction=polymorphism ref_cov=11/19 total_cov=20/25 RA 118 . USA300TCH1516_ALE 2405833 0 A G bias_e_value=2895040 bias_p_value=0.997231 consensus_score=128.3 fisher_strand_p_value=1 frequency=9.29470062e-02 ks_quality_p_value=0.926513 major_base=A major_cov=23/16 major_frequency=9.07052994e-01 minor_base=G minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.29470062e-02 polymorphism_score=5.0 prediction=polymorphism ref_cov=23/16 total_cov=25/18 RA 119 . USA300TCH1516_ALE 2425673 0 A G bias_e_value=2894210 bias_p_value=0.996946 consensus_score=137.5 fisher_strand_p_value=1 frequency=1.15665436e-01 ks_quality_p_value=0.922869 major_base=A major_cov=25/21 major_frequency=8.84334564e-01 minor_base=G minor_cov=3/3 new_cov=3/3 polymorphism_frequency=1.15665436e-01 polymorphism_score=11.2 prediction=polymorphism ref_cov=25/21 total_cov=28/24 RA 120 . USA300TCH1516_ALE 2451070 0 T C bias_e_value=2390130 bias_p_value=0.823308 consensus_score=114.6 fisher_strand_p_value=1 frequency=9.75403786e-02 ks_quality_p_value=0.46795 major_base=T major_cov=22/15 major_frequency=9.02459621e-01 minor_base=C minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.75403786e-02 polymorphism_score=6.0 prediction=polymorphism ref_cov=22/15 total_cov=24/17 RA 121 . USA300TCH1516_ALE 2462758 0 G A bias_e_value=2379440 bias_p_value=0.819625 consensus_score=85.5 fisher_strand_p_value=0.492069 frequency=2.49992371e-01 ks_quality_p_value=0.941194 major_base=G major_cov=11/22 major_frequency=7.50007629e-01 minor_base=A minor_cov=5/6 new_cov=5/6 polymorphism_frequency=2.49992371e-01 polymorphism_score=25.5 prediction=polymorphism ref_cov=11/22 total_cov=16/28 RA 122 . USA300TCH1516_ALE 2532298 0 A T consensus_score=212.7 frequency=1 major_base=T major_cov=14/45 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=14/45 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=14/45 RA 123 . USA300TCH1516_ALE 2532665 0 G T bias_e_value=2846870 bias_p_value=0.980638 consensus_score=138.3 fisher_strand_p_value=1 frequency=1.02644444e-01 ks_quality_p_value=0.809783 major_base=G major_cov=16/19 major_frequency=8.97355556e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=1.02644444e-01 polymorphism_score=5.6 prediction=polymorphism ref_cov=16/19 total_cov=18/21 RA 124 . USA300TCH1516_ALE 2568885 0 T A bias_e_value=2902560 bias_p_value=0.99982 consensus_score=137.8 fisher_strand_p_value=1 frequency=9.30323601e-02 ks_quality_p_value=0.981099 major_base=T major_cov=15/24 major_frequency=9.06967640e-01 minor_base=A minor_cov=2/2 new_cov=2/2 polymorphism_frequency=9.30323601e-02 polymorphism_score=6.0 prediction=polymorphism ref_cov=15/24 total_cov=17/26 RA 125 . USA300TCH1516_ALE 2615078 0 A G bias_e_value=1784060 bias_p_value=0.614539 consensus_score=98.6 fisher_strand_p_value=0.416443 frequency=1.70495033e-01 ks_quality_p_value=0.632035 major_base=A major_cov=27/12 major_frequency=8.29504967e-01 minor_base=G minor_cov=4/4 new_cov=4/4 polymorphism_frequency=1.70495033e-01 polymorphism_score=16.1 prediction=polymorphism ref_cov=27/12 total_cov=31/16 RA 126 . USA300TCH1516_ALE 2638727 0 C T bias_e_value=2896980 bias_p_value=0.9979 consensus_score=141.6 fisher_strand_p_value=1 frequency=8.70294571e-02 ks_quality_p_value=0.935894 major_base=C major_cov=25/17 major_frequency=9.12970543e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=8.70294571e-02 polymorphism_score=4.7 prediction=polymorphism ref_cov=25/17 total_cov=27/19 RA 127 . USA300TCH1516_ALE 2656802 0 A T bias_e_value=2654960 bias_p_value=0.914531 consensus_score=193.5 fisher_strand_p_value=1 frequency=6.41651154e-02 ks_quality_p_value=0.616152 major_base=A major_cov=30/29 major_frequency=9.35834885e-01 minor_base=T minor_cov=2/2 new_cov=2/2 polymorphism_frequency=6.41651154e-02 polymorphism_score=5.8 prediction=polymorphism ref_cov=30/29 total_cov=33/31 JC 128 . CP000731 1 1 CP000731 27041 -1 0 alignment_overlap=0 circular_chromosome=1 coverage_minus=43 coverage_plus=36 flanking_left=141 flanking_right=141 frequency=1 junction_possible_overlap_registers=129 key=CP000731__1__1__CP000731__27041__-1__0____141__141__0__0 max_left=135 max_left_minus=135 max_left_plus=132 max_min_left=68 max_min_left_minus=67 max_min_left_plus=68 max_min_right=66 max_min_right_minus=66 max_min_right_plus=63 max_pos_hash_score=260 max_right=133 max_right_minus=133 max_right_plus=130 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.72 new_junction_read_count=79 polymorphism_frequency=1.00000000e+00 pos_hash_score=48 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=129 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=129 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=79 JC 129 . CP000731 64 -1 CP000731 27041 -1 -33 alignment_overlap=-33 coverage_minus=3 coverage_plus=0 flanking_left=64 flanking_right=141 frequency=1.54861945e-01 junction_possible_overlap_registers=96 key=CP000731__64__-1__CP000731__27041__-1__-33__TTGTTATATTAAGTTTATTATAGCACTTTAAAT__64__141__0__0 max_left=35 max_left_minus=35 max_left_plus=0 max_min_left=35 max_min_left_minus=35 max_min_left_plus=0 max_min_right=0 max_min_right_minus=0 max_min_right_plus=0 max_pos_hash_score=194 max_right=81 max_right_minus=81 max_right_plus=0 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.04 new_junction_read_count=3 polymorphism_frequency=1.54861945e-01 pos_hash_score=3 prediction=polymorphism side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.40 side_1_overlap=0 side_1_possible_overlap_registers=129 side_1_read_count=44 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=129 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=3 unique_read_sequence=TTGTTATATTAAGTTTATTATAGCACTTTAAAT JC 130 . CP000731 6552 -1 CP000731 6553 1 -28 alignment_overlap=-28 coverage_minus=32 coverage_plus=36 flanking_left=141 flanking_right=141 frequency=1 junction_possible_overlap_registers=101 key=CP000731__6552__-1__CP000731__6553__1__-28__TCTCCAGGCACTTGTGCATATTCTGAAA__141__141__0__0 max_left=106 max_left_minus=106 max_left_plus=97 max_min_left=55 max_min_left_minus=44 max_min_left_plus=55 max_min_right=55 max_min_right_minus=55 max_min_right_plus=55 max_pos_hash_score=204 max_right=105 max_right_minus=95 max_right_plus=105 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.81 new_junction_read_count=69 polymorphism_frequency=1.00000000e+00 pos_hash_score=46 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=129 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=129 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=68 unique_read_sequence=TCTCCAGGCACTTGTGCATATTCTGAAA JC 131 . NC_012417 1 1 NC_012417 3125 -1 0 alignment_overlap=0 circular_chromosome=1 coverage_minus=293 coverage_plus=389 flanking_left=141 flanking_right=141 frequency=1 junction_possible_overlap_registers=129 key=NC_012417__1__1__NC_012417__3125__-1__0____141__141__0__0 max_left=135 max_left_minus=135 max_left_plus=135 max_min_left=70 max_min_left_minus=70 max_min_left_plus=70 max_min_right=69 max_min_right_minus=68 max_min_right_plus=69 max_pos_hash_score=260 max_right=135 max_right_minus=134 max_right_plus=135 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.83 new_junction_read_count=688 polymorphism_frequency=1.00000000e+00 pos_hash_score=181 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=129 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=129 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=682 JC 132 . USA300TCH1516_ALE 1 1 USA300TCH1516_ALE 2872915 -1 0 alignment_overlap=0 circular_chromosome=1 coverage_minus=23 coverage_plus=22 flanking_left=141 flanking_right=141 frequency=1 junction_possible_overlap_registers=129 key=USA300TCH1516_ALE__1__1__USA300TCH1516_ALE__2872915__-1__0____141__141__0__0 max_left=135 max_left_minus=135 max_left_plus=131 max_min_left=70 max_min_left_minus=70 max_min_left_plus=70 max_min_right=66 max_min_right_minus=61 max_min_right_plus=66 max_pos_hash_score=260 max_right=126 max_right_minus=126 max_right_plus=126 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.16 new_junction_read_count=45 polymorphism_frequency=1.00000000e+00 pos_hash_score=26 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=129 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=129 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=45 JC 133 . USA300TCH1516_ALE 512620 1 USA300TCH1516_ALE 2176447 1 -45 alignment_overlap=-45 coverage_minus=17 coverage_plus=12 flanking_left=141 flanking_right=141 frequency=5.14076359e-01 junction_possible_overlap_registers=84 key=USA300TCH1516_ALE__512620__1__USA300TCH1516_ALE__2176447__1__-45__TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAAC__141__141__0__0 max_left=89 max_left_minus=84 max_left_plus=89 max_min_left=44 max_min_left_minus=38 max_min_left_plus=44 max_min_right=45 max_min_right_minus=41 max_min_right_plus=45 max_pos_hash_score=170 max_right=83 max_right_minus=80 max_right_plus=83 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.22 new_junction_read_count=31 polymorphism_frequency=5.14076359e-01 pos_hash_score=20 prediction=polymorphism side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.00 side_1_overlap=0 side_1_possible_overlap_registers=129 side_1_read_count=39 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=129 side_2_read_count=51 side_2_redundant=0 total_non_overlap_reads=29 unique_read_sequence=TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAAC JC 134 . USA300TCH1516_ALE 895785 1 USA300TCH1516_ALE 909740 -1 0 alignment_overlap=17 coverage_minus=3 coverage_plus=6 flanking_left=141 flanking_right=141 frequency=2.20387244e-01 junction_possible_overlap_registers=112 key=USA300TCH1516_ALE__895785__1__USA300TCH1516_ALE__909757__-1__17____141__141__0__0 max_left=88 max_left_minus=61 max_left_plus=88 max_min_left=61 max_min_left_minus=61 max_min_left_plus=60 max_min_right=62 max_min_right_minus=0 max_min_right_plus=62 max_pos_hash_score=226 max_right=110 max_right_minus=110 max_right_plus=105 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.27 new_junction_read_count=9 polymorphism_frequency=2.20387244e-01 pos_hash_score=8 prediction=polymorphism side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.23 side_1_overlap=17 side_1_possible_overlap_registers=129 side_1_read_count=48 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.65 side_2_overlap=0 side_2_possible_overlap_registers=112 side_2_read_count=22 side_2_redundant=0 total_non_overlap_reads=9 JC 135 . USA300TCH1516_ALE 2085296 1 USA300TCH1516_ALE 2128343 -1 0 alignment_overlap=14 coverage_minus=3 coverage_plus=4 flanking_left=141 flanking_right=141 frequency=1.81398152e-01 junction_possible_overlap_registers=115 key=USA300TCH1516_ALE__2085296__1__USA300TCH1516_ALE__2128357__-1__14____141__141__0__0 max_left=94 max_left_minus=86 max_left_plus=94 max_min_left=52 max_min_left_minus=26 max_min_left_plus=52 max_min_right=41 max_min_right_minus=41 max_min_right_plus=33 max_pos_hash_score=232 max_right=112 max_right_minus=101 max_right_plus=112 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.20 new_junction_read_count=7 polymorphism_frequency=1.81398152e-01 pos_hash_score=5 prediction=polymorphism side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.67 side_1_overlap=14 side_1_possible_overlap_registers=129 side_1_read_count=26 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.15 side_2_overlap=0 side_2_possible_overlap_registers=115 side_2_read_count=40 side_2_redundant=0 total_non_overlap_reads=7 UN 136 . CP000731 12808 13050 UN 137 . CP000731 16516 16643 UN 138 . CP000731 16818 16989 UN 139 . CP000731 20816 20991 UN 140 . USA300TCH1516_ALE 36198 36261 UN 141 . USA300TCH1516_ALE 52603 52607 UN 142 . USA300TCH1516_ALE 52609 52766 UN 143 . USA300TCH1516_ALE 159582 159602 UN 144 . USA300TCH1516_ALE 458083 458083 UN 145 . USA300TCH1516_ALE 458087 458857 UN 146 . USA300TCH1516_ALE 512643 512643 UN 147 . USA300TCH1516_ALE 512806 512815 UN 148 . USA300TCH1516_ALE 513075 514298 UN 149 . USA300TCH1516_ALE 514589 514853 UN 150 . USA300TCH1516_ALE 515095 517596 UN 151 . USA300TCH1516_ALE 557082 558589 UN 152 . USA300TCH1516_ALE 558591 558591 UN 153 . USA300TCH1516_ALE 558899 558899 UN 154 . USA300TCH1516_ALE 558901 561955 UN 155 . USA300TCH1516_ALE 1457288 1457642 UN 156 . USA300TCH1516_ALE 1457644 1457644 UN 157 . USA300TCH1516_ALE 1601441 1601446 UN 158 . USA300TCH1516_ALE 1601448 1601484 UN 159 . USA300TCH1516_ALE 1803421 1803421 UN 160 . USA300TCH1516_ALE 1803425 1803431 UN 161 . USA300TCH1516_ALE 1803442 1803442 UN 162 . USA300TCH1516_ALE 1803455 1803455 UN 163 . USA300TCH1516_ALE 1911232 1911232 UN 164 . USA300TCH1516_ALE 1911236 1911237 UN 165 . USA300TCH1516_ALE 1911239 1911267 UN 166 . USA300TCH1516_ALE 1911271 1911271 UN 167 . USA300TCH1516_ALE 1917908 1918253 UN 168 . USA300TCH1516_ALE 1937664 1938449 UN 169 . USA300TCH1516_ALE 1994377 1994377 UN 170 . USA300TCH1516_ALE 1994379 1995362 UN 171 . USA300TCH1516_ALE 1998415 1998415 UN 172 . USA300TCH1516_ALE 1998417 1998417 UN 173 . USA300TCH1516_ALE 1998419 1999704 UN 174 . USA300TCH1516_ALE 1999941 2000836 UN 175 . USA300TCH1516_ALE 2001292 2001499 UN 176 . USA300TCH1516_ALE 2001502 2001502 UN 177 . USA300TCH1516_ALE 2001506 2001506 UN 178 . USA300TCH1516_ALE 2001511 2001513 UN 179 . USA300TCH1516_ALE 2001515 2001516 UN 180 . USA300TCH1516_ALE 2001518 2001518 UN 181 . USA300TCH1516_ALE 2001922 2002032 UN 182 . USA300TCH1516_ALE 2002510 2003395 UN 183 . USA300TCH1516_ALE 2003409 2003409 UN 184 . USA300TCH1516_ALE 2003418 2003418 UN 185 . USA300TCH1516_ALE 2003420 2003420 UN 186 . USA300TCH1516_ALE 2121955 2121955 UN 187 . USA300TCH1516_ALE 2121957 2122001 UN 188 . USA300TCH1516_ALE 2176703 2181114 UN 189 . USA300TCH1516_ALE 2181341 2181341 UN 190 . USA300TCH1516_ALE 2181345 2181418 UN 191 . USA300TCH1516_ALE 2254817 2254848 UN 192 . USA300TCH1516_ALE 2290820 2291789 UN 193 . USA300TCH1516_ALE 2292883 2297653 UN 194 . USA300TCH1516_ALE 2319274 2319275 UN 195 . USA300TCH1516_ALE 2319277 2319283 UN 196 . USA300TCH1516_ALE 2319285 2319295 UN 197 . USA300TCH1516_ALE 2624068 2624173 UN 198 . USA300TCH1516_ALE 2624427 2624600