Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
MC JC	ACB122	4,963,095	Δ12,336 bp	100%		[CJ019_04659]–[flgE]	[CJ019_04659], fabH, CJ019_04661, CJ019_04662, CJ019_04663, flgI, flgH, flgG, flgF, CJ019_04668, [flgE]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	ACB122	4963095	4975430	12336	46 [0]	[0] 47	[CJ019_04659]–[flgE]	[CJ019_04659],fabH,CJ019_04661,CJ019_04662,CJ019_04663,flgI,flgH,flgG,flgF,CJ019_04668,[flgE]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	ACB122	= 4963094	0 (0.000)	35 (0.710)	28/206	NT	100%	coding (1114/2064 nt)	CJ019_04659	hypothetical protein
	?	ACB122	4975431 =	0 (0.000)					coding (489/1323 nt)	flgE	Flagellar hook protein FlgE

AGTTGAAGGTAGTGCCATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  ACB122/4962947‑4963094 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcagccgagttcagGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACCCTGCAGGTTGGCACCCGAAGC  >  ACB122/4975431‑4975565                                                                                                                                                                                                                                                                                             AGTTGAAGGTAGTGCCATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGG                                                                                                                                                      <  1:215823/135‑1    TGAAGGTAGTGCCATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAG                                                                                                                                                   >  2:312590/1‑135    TGAAGGTAGTGCCATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAG                                                                                                                                                   >  2:206036/1‑135           AGTGCCATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGT                                                                                                                                             >  6:310600/1‑134              GCCATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGACCCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGG                                                                                                                                        >  8:356100/1‑136                CATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTT                                                                                                                                      >  7:332639/1‑136                CATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTT                                                                                                                                      >  3:133184/1‑136                CATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGT                                                                                                                                       >  5:112401/1‑135                 ATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTT                                                                                                                                      <  1:84552/135‑1                      TGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTT                                                                                                                                <  7:318494/136‑1                         CGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTC                                                                                                                               <  5:225080/134‑1                              GAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGA                                                                                                                        >  3:343714/1‑136                                     CCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCT                                                                                                                 <  4:82547/136‑1                                        ACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGT                                                                                                              >  3:267023/1‑136                                                  GGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCCGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGG                                                                                                     <  6:141288/135‑1                                                  GGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGG                                                                                                     >  1:189756/1‑135                                                  GGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGCCCAGTCAACGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGG                                                                                                     >  5:50019/1‑135                                                      GTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCG                                                                                                   >  6:193967/1‑133                                                            GGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGATCAGGTTGATCTTCACGGTGCTGAGGCTGGTCGGCTTCGGCGTCAGGTTG                                                                                           >  6:234949/1‑135                                                              CGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCA                                                                                                                                                    >  3:24020/1‑76                                                              CGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCA                                                                                                                                                    <  4:24020/76‑1                                                                   TGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTAT                                                                                    >  2:12656/1‑135                                                                          AGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGC                                                                            <  8:51662/136‑1                                                                           GAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGACGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGC                                                                            <  6:112401/135‑1                                                                            AACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCA                                                                           <  6:300234/135‑1                                                                            AACATGCAGTAAGACCCCGGCCAGTCAAGGTACCCGCATAACAACCTACGGCGAAGCCGGCAGCCGAGTTCAGTTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCA                                                                           <  4:133184/135‑1                                                                             ACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAG                                                                          <  1:312590/135‑1                                                                                     gcaccCCCAGGCCTGTCAAGGCACCGGCCGAACCACCTCCGTCGAACCCGGCAGCCGAGTGCCGGTTGTTCTTCTCGGTGATGAGGCGGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCA                                                                  <  1:386523/130‑1                                                                                        GACCCAGGCCAGGCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGAT                                                              <  7:287321/136‑1                                                                                         ACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGGCAGGTTGGAAGTCTCCTTCTGCAGGTGAGTCAGGCTG                                                             >  7:336399/1‑136                                                                                          CCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGC                                                            >  7:277105/1‑136                                                                                                      AAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCT                                                >  8:293736/1‑136                                                                                                            CCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGT                                          >  8:203416/1‑136                                                                                                                CAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTGGATCTTCTCGGTGAGGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTC                                      <  7:190699/136‑1                                                                                                                 AGTCCCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTC                                      <  6:142548/135‑1                                                                                                                 AGTCCCACCTACGTCCTAGCCGGCCGCCGCGTTCTGGTTGATCTTCTGGGTGATGAGGGTGGGCGGGTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTC                                      <  6:3453/135‑1                                                                                                                   TACCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGTGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGC                                    <  6:372006/135‑1                                                                                                                     CCACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGA                                 >  7:262894/1‑136                                                                                                                       ACCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGGCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACC                               <  7:86113/136‑1                                                                                                                        CCTACGTCGATGCCGGCTGCCGAGTTAAGGTTGATCTTGTCGGTGATGAGGCTGGTCGGGTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCG                              <  7:162774/136‑1                                                                                                                        CCTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACC                               <  1:12656/135‑1                                                                                                                         CTACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGGCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCG                              <  2:51023/135‑1                                                                                                                           ACGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGC                             >  1:119047/1‑134                                                                                                                            CGTCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCA                            <  7:203416/134‑1                                                                                                                              TCGAAGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAc                         >  1:173684/1‑134                                                                                                                                GAAGCCGGCAGCCGAGTTCAGGGTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACC                       >  2:238903/1‑135                                                                                                                                  AGCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACCCT                     >  2:172399/1‑135                                                                                                                                   GCCGGCAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACCCTG                    >  8:12791/1‑135                                                                                                                                       GCAGCGGTGTTCAGGTTGATCTTCTCGCTTATGAGGCTGGGCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACCCTGCAGGT               <  7:356100/136‑1                                                                                                                                        CAGCCGAGTTCAGGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACCCTGCAGGT               <  5:301569/135‑1                                                                                                                                                 tccGGTTGATCTTCTCGGTGATGAGGCTGGGCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACCCTGCAGGTTGGCACCCG      <  1:241420/132‑1                                                                                                                                                    GGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACCCTGCAGGTTGGCACCCGAAGC  <  3:267175/136‑1                                                                                                                                                                                                                                                                                             AGTTGAAGGTAGTGCCATTGATGTCGATCGAAGCAGCCGACGCCAGACCGGTAGTCTGAGGCGCGATGGCAACAGAACCTGCAGTCAGACCCAGGCCAGTCAAGGTACCCGCAGTACCACCTACGTCGAAGCCGGCAGCCGAGTTCAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  ACB122/4962947‑4963094 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcagccgagttcagGTTGATCTTCTCGGTGATGAGGCTGGTCGGCTTCGGCGTCAGGTTGGAAGTATCGATCTGCAGGTCAGTCAGGATGCCCTGGATGATCTTGCCGTCCTCGCCGACCGCATAACCCTGCAGGTTGGCACCCGAAGC  >  ACB122/4975431‑4975565

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.