Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	257,908	Δ776 bp		insB9–[crl]	insB9, insA9, [crl]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	257908–258676	258683	8–776	32 [1]	[1] 32	insB9–[crl]	insB9,insA9,[crl]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 257907	1 (0.020)	31 (0.550)	31/476	0.7	98.5%	intergenic (+8/+16)	crl/insB9	RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B
	?	NC_000913	258684 =	0 (0.000)					pseudogene (9/331 nt)	crl	RNA polymerase holoenzyme assembly factor Crl

TAAATTATTAGAGATCCCATTTAACCCGGTGTATCGGAATTTTGACAAAGGTCTTCAGGAAATCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTG  >  NC_000913/257678‑258155                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                         tAAATTATTAGAGATCCCATTTAACCCGGTGTATCGGAATTCTGACAAAGGTCTTCAGGAAATCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattct                                                                                                                                                                                                                                     >  1:287795‑M1/1‑230 (MQ=255)    attattAGCGATCCCATTTAACCCGGTGTATCGGAATTTTGACAAAGGTCTTCAGGAAATCACCGACTGGATCGCACAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCCATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGCGTGGACACCCGAAGAGCAGACTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagagcaaagataatcgattctttt                                                                                                                                                                                                                                  >  1:372689‑M1/1‑227 (MQ=255)      tattaGAGATCCCATTTAACCCGGTGTATCGGAATTTTGACAAAGGTCTTCAGGAAATCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttc                                                                                                                                                                                                                                >  1:549265‑M1/1‑225 (MQ=255)                       aaCCCGGTGTATCGGAATGTTGACAAAGGTCTTCAGGAAATCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatg                                                                                                                                                                                                               <  2:448320‑M1/251‑44 (MQ=255)                        aCCCGGTGTATCGGAATTTAGACAAAGGTATTCAGGAAATCCCCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcacagataatcgattctttttcgattgtctggctgtatgc                                                                                                                                                                                                              >  1:209838‑M1/1‑207 (MQ=255)                         cccGGTGTCTCGGAATTATGACAACGGTCTTCAGGAAATCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAACGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgcttctttttcgattgtctggatgtatgcg                                                                                                                                                                                                             >  2:271753‑M1/1‑206 (MQ=255)                                                                        ggATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggg                                                                                                                                                                      <  2:409456‑M1/243‑85 (MQ=255)                                                                        ggATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggg                                                                                                                                                                      >  1:409456‑M1/1‑159 (MQ=255)                                                                         gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTGGGTAAAACAGTTGCAGCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcggcaacgtgaaaccggctccggaagtgcgtgaattctggggctggtgga                                                                                                                                                             <  1:423035‑M1/251‑94 (MQ=255)                                                                                  aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctgtttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctgg                                                                                                                                                    <  1:70965‑M1/251‑103 (MQ=255)                                                                                       tgtgTTAAAAATTTGCTAAATGTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTGCCGAGTGGACTCCCGAAGAGCAGATTTATCAAAAAATTTACCGCACTAGGCCCGTATATGCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcagcggaagtgcgtgaattctggggctggtggagggagctggaag                                                                                                                                                 <  2:217111‑M1/249‑106 (MQ=255)                                                                                             aaaaaTATGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGCTACCGAGTCGACACCCGAAGAGCAGATTGGTCAAACAATTTACCGCACTAGGCCCGTATATTCGAGAAGGTAagtgcaaagataatcgattctttttcgattgtctggatgtatgcgtcaacgtgcaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcagga                                                                                                                                          >  1:384607‑M1/1‑138 (MQ=255)                                                                                                     gCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttt                                                                                                                                 <  2:118437‑M1/251‑122 (MQ=255)                                                                                                                ccAATTTGGTAAAACCGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTAATCAAACAATTTACCGCAATAGGCCCGGATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaagccggccccggaagagagtgaattctggggctgggggatggagctggaagcgcaggaatcccgttttaactac                                                                                                                          >  1:373445‑M1/1‑119 (MQ=255)                                                                                                                   aTTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttacc                                                                                                                   >  1:408056‑M1/1‑116 (MQ=255)                                                                                                                       ggTAAAACAGTTGCATCACAACAGGAGATACCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtt                                                                                                               >  1:215800‑M1/1‑112 (MQ=255)                                                                                                                             aCAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtct                                                                                                         <  1:405545‑M1/251‑146 (MQ=255)                                                                                                                                              ggAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcg                                                                                        >  1:214740‑M1/1‑89 (MQ=255)                                                                                                                                                       aaTGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactgga                                                                                  >  1:406679‑M1/1‑80 (MQ=255)                                                                                                                                                             gTTACCGAGTGGACACCCGCAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGACGGTAattgcaaagataatcgattctttttcgattgtctggctgaatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtgggtggagctggaagcgcaggaatcccgttgtacctacagttaccagtttggtctgttcgctaaagcaggcgactggaagagtgttc                                                                         >  1:331554‑M1/1‑74 (MQ=255)                                                                                                                                                               tACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagctaatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagggttccg                                                                       >  2:461712‑M1/1‑72 (MQ=255)                                                                                                                                                                  cGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTCGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggt                                                                     >  1:247141‑M1/1‑69 (MQ=255)                                                                                                                                                                                              cAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactg                                         <  2:17260‑M1/250‑210 (MQ=255)                                                                                                                                                                                                   aaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctgtttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatgtagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactggagcac                                   <  1:517333‑M1/251‑216 (MQ=255)                                                                                                                                                                                                        aCCGCCCTAGGCCCGTATATGCGTGAAGGTAagtgcaaagataatcgattcgttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactggagcactccct                              <  2:408335‑M1/251‑221 (MQ=255)                                                                                                                                                                                                          cGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactggagcacaccctgc                            >  2:164623‑M1/1‑29 (MQ=255)                                                                                                                                                                                                           gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactggagcacaccctgcg                           >  1:427888‑M1/1‑28 (MQ=255)                                                                                                                                                                                                             aCTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactggagcacaccctgcgtg                         >  2:428030‑M1/1‑26 (MQ=255)                                                                                                                                                                                                                    ccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggaggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactggagcacaccctgcgtgagtttc                   >  1:575264‑M1/1‑19 (MQ=255)                                                                                                                                                                                                                        atatTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactggagcacaccctgcgtgagtttcacg                >  1:79713‑M1/1‑15 (MQ=255)                                                                                                                                                                                                                             cGTGAAGGTAagtgcaaagataattgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgttcgataaagcaggcgactggaagagtgttccggtaaaagacactgaagtggttgaacgactggagcacaccctgcgtgagtttcacgagaagc          <  1:301199‑M1/250‑241 (MQ=255)                                                                                                                                                                                                                                     taggtaATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATCTCACCACGTCAAAGGGTg  >  1:1545/1‑250 (MQ=11)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                         TAAATTATTAGAGATCCCATTTAACCCGGTGTATCGGAATTTTGACAAAGGTCTTCAGGAAATCACCGACTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTG  >  NC_000913/257678‑258155

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑