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	39 [0]	[0] 38	[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)	35 (1.040)	30/262	0.2	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

ACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCG  >  NC_000913_3_pae_tpiA/3815795‑3816089                                                                                                                                                   |                                                                                                                                                     tttaacacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaacaatcagtttgccagcgccgccttctgcCGt                                                                                                                                                    >  1:517925‑M2/147‑149 (MQ=255)  ttaacacctgcttcctaagcgcaatttcaatgagctttggctgatatagtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcttcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTc                                                                                                                                                   <  1:245561‑M2/4‑1 (MQ=255)    aacacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTccc                                                                                                                                                 <  2:44561‑M2/6‑1 (MQ=255)     acacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTcccc                                                                                                                                                >  2:70969‑M2/143‑149 (MQ=255)         ctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctccgcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCa                                                                                                                                            >  1:520104‑M2/139‑149 (MQ=255)               gctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaataagtttgccagcgccgccttctgcCGTCCCCTGCACTTCaa                                                                                                                                      <  2:628693‑M2/17‑1 (MQ=255)                  aagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAatga                                                                                                                                   <  1:8272‑M2/20‑1 (MQ=255)                   agcccaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAatgat                                                                                                                                  <  1:514320‑M2/21‑1 (MQ=255)                      gcaaattcaataaactggggcttatatggtttcatgcctgcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATgcg                                                                                                                               <  2:520104‑M2/24‑1 (MQ=255)                              aataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                                                                                                                       >  2:572136‑M2/118‑149 (MQ=255)                                  aactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                                                                                                   <  1:303033‑M2/36‑1 (MQ=255)                                   actggcggtgagatggttttctgccttcgctcctcatcgtacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAAGGATGCGCCCGTCTTCGGtc                                                                                                                  <  2:78011‑M2/37‑1 (MQ=255)                                           ggatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTAc                                                                                                          <  2:429029‑M2/45‑1 (MQ=255)                                                 ggtttcatgccttcgcccctcatcttacttttccacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCAt                                                                                                    <  1:75272‑M2/51‑1 (MQ=255)                                                 ggttgcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCAt                                                                                                    <  2:107376‑M2/51‑1 (MQ=255)                                                       atgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                                                                                              >  1:22478‑M2/93‑149 (MQ=255)                                                       atgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                                                                                              >  1:22306‑M2/93‑149 (MQ=255)                                                       atgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                                                                                              >  1:21683‑M2/93‑149 (MQ=255)                                                        tgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtc                                                                                             >  2:27690‑M2/92‑149 (MQ=255)                                                               gctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCgg                                                                                      <  1:572136‑M2/65‑1 (MQ=255)                                                                   ctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTCCGTTCATGTCGGTCTCTGCGGcagc                                                                                  >  1:588232‑M2/81‑148 (MQ=255)                                                                   ctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga                                                                                  <  2:605189‑M2/69‑1 (MQ=255)                                                                      atcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGTTCATCACTACGTTCATGTCGGTCTCTGCGGCAGGGTc                                                                               >  1:28822‑M2/78‑149 (MQ=255)                                                                             ttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagtgccgccttctgaCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTGCGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACg                                                                        >  1:225197‑M2/71‑149 (MQ=255)                                                                                  tacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTc                                                                   >  2:162849‑M2/66‑149 (MQ=255)                                                                                  tacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTc                                                                   >  2:281779‑M2/66‑149 (MQ=255)                                                                                       acaaaaaggaggcgactcatgtgttggcttaaaaatcagtttgccggcgcggccttttgcCGTCCCCGGCACTTCAGTGATGCGCCGGTCTTCGGTCATCACTGCGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGAt                                                              <  2:422464‑M2/89‑1 (MQ=255)                                                                                       acaaaaaaaaggcgcctcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGAt                                                              <  1:70969‑M2/89‑1 (MQ=255)                                                                                              aaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCTTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAAc                                                       <  1:281779‑M2/96‑1 (MQ=255)                                                                                                 ggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAAATCGCAAACCGc                                                    >  1:186507‑M2/51‑149 (MQ=255)                                                                                                       tcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGcc                                              <  1:162849‑M2/105‑1 (MQ=255)                                                                                                         atcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCCGATCGCGAACCGCTTcgccat                                            >  1:31721‑M2/43‑147 (MQ=255)                                                                                                                                  ccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAg                                                                <  2:501827‑M2/87‑1 (MQ=255)                                                                                                                                  ccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAg                                                                >  1:501827‑M2/18‑104 (MQ=255)                                                                                                                                        ccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCAGTTCACAATTCCGACAGAAACTGCGGCTACCAt             >  1:205074‑M2/12‑149 (MQ=255)                                                                                                                                         cgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATc            >  1:414275‑M2/11‑149 (MQ=255)                                                                                                                                            cttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCt         <  1:207538‑M2/142‑1 (MQ=255)                                                                                                                                                   cGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCg  >  1:274043/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                     ACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCG  >  NC_000913_3_pae_tpiA/3815795‑3816089

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: ‑