Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	3,815,859	Δ82 bp		[rph]–[rph]	[rph], [rph]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_pae_tpiA	3815859	3815940	82	47 [0]	[0] 47	[rph]–[rph]	[rph],[rph]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 3815858	0 (0.000)	44 (0.890)	39/264	0.3	100%	pseudogene (24/48 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
	?	NC_000913_3_pae_tpiA	3815941 =	0 (0.000)					pseudogene (609/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

CTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGC  >  NC_000913_3_pae_tpiA/3815712‑3816006                                                                                                                                                   |                                                                                                                                                     cTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCATAACATTTAGTTAGCCAGCGCCGCCTTCTGCcg                                                                                                                                                    >  2:193403‑M1/1‑147 (MQ=255)     aaCACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtccc                                                                                                                                                <  1:298560‑M1/149‑7 (MQ=255)        acCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctg                                                                                                                                             >  2:811357‑M1/1‑140 (MQ=255)         ccTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAATTTGGCCGCGCTGCCTTCTGCcgtccccggc                                                                                                                                            >  1:912815‑M1/1‑139 (MQ=255)                gctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAACAAGGCGACTCATCAGTCGCCTTAAACATCAGTTTGCCAGCGCCGCCTTCTGCcgtccccggcacttcca                                                                                                                                     >  1:63545‑M1/1‑132 (MQ=255)                cataaCCGCAAATTCAATAAACCGGCGCTGATATGGTTTCACGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCCCCTTAAAACTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaa                                                                                                                                     <  1:716494‑M1/147‑18 (MQ=255)                 ctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCATTTTGCCAGCACCTCCTTCTGCcgtcccctgcacttcaat                                                                                                                                    >  1:353504‑M1/1‑131 (MQ=255)                 ctAAGCGCAAACTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaat                                                                                                                                    <  1:189382‑M1/149‑19 (MQ=255)                 ccaagcGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCACCGCCTTCTGCcgtcccctgcacttcaat                                                                                                                                    >  1:353481‑M1/3‑131 (MQ=255)                    aGCGCAAATTCAATAAACTGGCGCAGATCTGAAGAGAGTCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgat                                                                                                                                 >  2:441425‑M1/1‑128 (MQ=255)                      cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgc                                                                                                                               >  1:606973‑M1/1‑126 (MQ=255)                       gcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtccctgcacttcaatgatgcgc                                                                                                                              >  1:112852‑M1/1‑125 (MQ=255)                       gcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgccccctgcacttccatgatgca                                                                                                                              >  1:484650‑M1/1‑125 (MQ=255)                        cAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgc                                                                                                                             <  2:730614‑M1/149‑26 (MQ=255)                          aaTTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAACAAAGGCGACTCATCAGTCGCCTTCAAAATCTGCTTGCCACCGCCGCCTTCTGCcgtcccccgcccttccatcatgccccc                                                                                                                           >  2:725053‑M1/1‑122 (MQ=255)                                    aCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtc                                                                                                                 <  2:698319‑M1/149‑38 (MQ=255)                                      tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTGCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcat                                                                                                               >  2:821136‑M1/1‑110 (MQ=255)                                        gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatca                                                                                                             <  1:40829‑M1/149‑42 (MQ=255)                                             gATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacg                                                                                                        >  1:790050‑M1/1‑103 (MQ=255)                                              atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTCCATACAAACAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTCCCAGCGCCGCCTTCTACcgtcccctgcacttcaatgatgcgcccgtcttcgctaatcactactt                                                                                                       >  2:614915‑M1/1‑102 (MQ=255)                                              atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgt                                                                                                       >  1:395257‑M1/1‑102 (MQ=255)                                                atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttc                                                                                                     >  1:482705‑M1/1‑100 (MQ=255)                                                      tCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcg                                                                                               <  2:837337‑M1/149‑56 (MQ=255)                                                      tCATGCCTTCGCCCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcg                                                                                               <  2:173577‑M1/149‑56 (MQ=255)                                                           ccTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctc                                                                                          >  1:315458‑M1/1‑89 (MQ=255)                                                                  tcctcATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcactgatgcgcccgtcttcggtaatcacgacgttcatatcgtgctctgcggca                                                                                   >  2:401340‑M1/1‑82 (MQ=255)                                                                    ctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtctttggtcatcactacgttcatgtcggtctctgcggcaga                                                                                 >  1:175601‑M1/1‑80 (MQ=255)                                                                    ctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAACGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtactcactacgttcatgtcggtctctgcggccgc                                                                                 >  2:405290‑M1/1‑80 (MQ=255)                                                                    cacaccttactTCCCTACAGACAAAAAAAAGGCGACTCCTCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcaga                                                                                 <  1:24949‑M1/144‑70 (MQ=255)                                                                       aTCTTGCGTTTCGACAGACAAAAAAAAGGCGTCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgctcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtc                                                                              <  2:518418‑M1/149‑73 (MQ=255)                                                                        tCTTACCTTTCCACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtct                                                                             <  1:932653‑M1/149‑74 (MQ=255)                                                                         cTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgctgcgcccgtcttcggtcctcactacgttcatgtcggtctctgcggcagagtctt                                                                            >  1:209188‑M1/1‑75 (MQ=255)                                                                                       gACAAAAAAAAGGCGACTCATCAGTCGCCTTAAACATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccaga                                                              <  1:114646‑M1/149‑89 (MQ=255)                                                                                             aaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaa                                                        >  2:290236‑M1/1‑55 (MQ=255)                                                                                                   gCGACTGATGAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgct                                                  >  1:765694‑M1/1‑49 (MQ=255)                                                                                                          atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgt                                           <  2:658164‑M1/149‑108 (MQ=255)                                                                                                               tCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttaatgtcggtgttacctgcagagccttcaacgtattccagatcgcaaaccgcttcgccgttcaca                                      >  1:648905‑M1/1‑37 (MQ=255)                                                                                                                cGCCTTAAAAATCTGTTGTCCAGCTCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcacttcgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaa                                     <  1:193403‑M1/149‑114 (MQ=255)                                                                                                                       aaaaTCTGTGTGCCAGCGCCGTCTTCTGCcgtcccctgcacttcaatgatgcgcccttcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgac                              <  2:65839‑M1/149‑121 (MQ=255)                                                                                                                             aGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaac                        >  1:354710‑M1/1‑23 (MQ=255)                                                                                                                               tttGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagt                                                                               >  2:426532‑M1/1‑21 (MQ=255)                                                                                                                               tttGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagt                                                                               <  1:426532‑M1/92‑72 (MQ=255)                                                                                                                               gttgCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactg                      <  1:531215‑M1/148‑129 (MQ=255)                                                                                                                                         ccgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccat            <  2:606973‑M1/149‑139 (MQ=255)                                                                                                                                              ttCTGCcgtcccctgcatttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccatccctt       <  2:536668‑M1/149‑144 (MQ=255)                                                                                                                                              ttCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccatccctt       >  1:605002‑M1/1‑6 (MQ=255)                                                                                                                                                   ccgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccatccctttcatc  <  2:354710‑M1/149‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                     CTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGC  >  NC_000913_3_pae_tpiA/3815712‑3816006

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑