Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	3,815,859	Δ82 bp		[rph]–[rph]	[rph], [rph]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3815859	3815940	82	41 [0]	[0] 40	[rph]–[rph]	[rph],[rph]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3815858	0 (0.000)	35 (0.980)	32/264	0.1	100%	pseudogene (24/48 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
	?	NC_000913	3815941 =	0 (0.000)					pseudogene (609/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

AACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTC  >  NC_000913/3815716‑3816000                                                                                                                                               |                                                                                                                                               accacctGCTTGCTAAGCGCAACTTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCCCATCGTACTTCTCTACAGACAAAAAACAGTCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGC                                                                                                                                                <  2:568953‑M1/141‑1 (MQ=255) aaCACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGC                                                                                                                                                <  2:314170‑M1/143‑1 (MQ=255)       ggcttgctaGCCTCTAGTTTAATACACTGGCCCTGGTGTGGTTTCATGCCTTCGCTCCTGATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCTGTTTGCCAGCGCCGCCTTCTGCcgtccc                                                                                                                                          <  2:554402‑M1/142‑7 (MQ=255)           tgctAAGCGCAAATCCAATAAACTGGCGCTGATATGGTTTCATGCCGTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgc                                                                                                                                      <  1:611076‑M1/143‑11 (MQ=255)              tAAGCGCAAAGTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCCGCcgtcccctgcaat                                                                                                                                   <  2:398563‑M1/143‑14 (MQ=255)               aaGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGACGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctcgtctt                                                                                                                                  >  1:187805‑M1/1‑129 (MQ=255)               aaGCGCAAAATTACGAAACTGGCGAGAATATAGATACAAGCCGTCGCTCCTCATCTTACTTATCTACAGCCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcactt                                                                                                                                  <  1:146149‑M1/143‑15 (MQ=255)                aGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAGAAAAAAGGCGACTCATCAGTCGCCTTACAAACACGTTTCCCAACGCCGCCTTCTGCcggcccctgccctcg                                                                                                                                 >  1:491898‑M1/1‑128 (MQ=255)                  ctcaaATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaa                                                                                                                               <  2:719991‑M1/141‑18 (MQ=255)                  cgtaaattcAATAAACTGACGCTGATATGGTTGCAGGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaa                                                                                                                               <  1:88101‑M1/140‑18 (MQ=255)                      aaTTGAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgat                                                                                                                           <  2:330128‑M1/143‑22 (MQ=255)                       aTTCAATAACCTGGCGCTGATATGGTTTCATGCCTTCGCACCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatg                                                                                                                          <  1:476394‑M1/143‑23 (MQ=255)                                     agcagagatggtgacaTGCCTTCGCTCCACCTCTTACTTTTCGACAGACAAAAAAAAGGCGACTCATCAGTCGTCTTAAAACTCAGTTTGCCAGCGCCGCCTTCTGCcgacccctgcacttcaatgatgcgcccgtcttcggt                                                                                                            <  1:287345‑M1/136‑37 (MQ=255)                                               ggttgatgtctTCGGTCTTCATCTTATGTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAATTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacg                                                                                                  <  2:204870‑M1/138‑47 (MQ=255)                                                            gCTCCTCATCTTATTTTTCTACATACTAAAAATAGGCGTCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTGCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtct                                                                                     <  1:341959‑M1/143‑60 (MQ=255)                                                            gCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactaagatcatgacggtct                                                                                     >  2:417161‑M1/1‑84 (MQ=255)                                                             gccctcagATTACTTTTCTACAGACAGAAAAAATGCGTCTCTTCAGTCGCCTTAAAAATCATTTTGCTAGCCCCGCCTTCTGCcgtcccctgcacttcaatgatgcgctcgtcttcggtcatcactacgttcatgtcggtctc                                                                                    <  2:319882‑M1/141‑61 (MQ=255)                                                             ctcctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGACGCCTTCTGCcgtcccctgcacttcaatgctgcgcccgtcttcggtcatcactacgatcatgtcggtctc                                                                                    >  2:234070‑M1/1‑83 (MQ=255)                                                              tcctcATCTTACTTTTCTACAGACAAAAAACACGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctct                                                                                   <  2:363856‑M1/143‑62 (MQ=255)                                                                           ttgctacAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCAAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtctt                                                                      <  2:683693‑M1/140‑75 (MQ=255)                                                                              ttacatacaaAAAAAAGGCGATTCTTCAGTCGCTTTAATAATCATTTTGCCAGCGCCGCATTCTGCcggcccctgcactgcaatgatgcgcccggcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaa                                                                   <  1:205416‑M1/142‑78 (MQ=255)                                                                              cTACAGACAAAAAAAAGGCTACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaa                                                                   <  1:718811‑M1/143‑78 (MQ=255)                                                                               tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgttcgctgcacttcaatgttgcgcccgttttcggtcatcactacgttcatgtagtgctccacggcagagacttcacc                                                                  >  1:146784‑M1/1‑65 (MQ=255)                                                                                    aCAAAAAAAAGGCGACTCTTCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgaagcgcccctcttcggtcatcactaagttcatgtcggtctctgcggcaaagactccaaacaact                                                             >  2:231906‑M1/1‑60 (MQ=255)                                                                                      aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcacgacgttcatgtcggtctctgcagcagagtcgtcaacgaattcc                                                           >  2:237899‑M1/1‑58 (MQ=255)                                                                                       aaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcccttcaatgatgcgcccgtcttcggtaaacactacaatcataccggactctagggcaaagtcttcaaagtattcca                                                          >  1:421611‑M1/1‑57 (MQ=255)                                                                                          ataaggCGACTCATCAGTCGGGTTAAAGAGCAGATCGGCGGCGCCTCGTCCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagat                                                       <  1:328270‑M1/141‑90 (MQ=255)                                                                                                  atccatcagtcGCCTTAAAAATCAGTTTGCCTGCGCCACCTTCTGCcgtcccctgcacttcattgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtatttcagatcgcaaacc                                               <  2:93318‑M1/140‑98 (MQ=255)                                                                                                          gTCGCCTTAAAAATCAGTTTGCCAGCGCCGACTTCTGCcgtcccctgcacttcaatgatgcgcccgtcatcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaacgcaacgcc                                       >  2:28179‑M1/1‑38 (MQ=255)                                                                                                           tCGCCATAAAAAGCAGTGTGCCAGCGCCGCCTTCTGCcggcgcctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccg                                      <  1:690338‑M1/143‑107 (MQ=255)                                                                                                                  aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcatttctatgattcgcccgtcttcgttcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaa                               <  1:265995‑M1/143‑114 (MQ=255)                                                                                                                   aaaaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatccctacgttcatgtcggtctctgcggcagagcctccaacgtactccagcccgcaaaccccttcgccgtccacaat                              >  2:490615‑M1/1‑29 (MQ=255)                                                                                                                        cAGTTTGCCAGCGCCCCTTTCTGCcgtctcctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccga                         <  2:189418‑M1/143‑120 (MQ=255)                                                                                                                           tttGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcagtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacag                      >  1:376062‑M1/1‑21 (MQ=255)                                                                                                                             tGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtctccggtcatcactacgttcatgacggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgctcacaattacgccagaa                    >  2:296328‑M1/1‑19 (MQ=255)                                                                                                                               ccAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacacttccgacagaaac                  >  2:456515‑M1/1‑17 (MQ=255)                                                                                                                                   cgccgcCTTCTGCcgtcgcctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcg              <  2:612193‑M1/143‑131 (MQ=255)                                                                                                                                      cgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggct           <  1:591892‑M1/143‑134 (MQ=255)                                                                                                                                      cgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgctcatgtcggtctctgcggcagagtcttcaacgtattacagatagcaaaccacttagccgatcacaattccgacagaaactgcggat           >  1:677540‑M1/1‑10 (MQ=255)                                                                                                                                          ttCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagagcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctacca       <  1:71595‑M1/143‑138 (MQ=255)                                                                                                                                               ccgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagcgtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggctaccatccct  >  1:601738‑M1/1‑1 (MQ=255)                                                                                                                                               |                                                                                                                                               AACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTC  >  NC_000913/3815716‑3816000

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑