Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	NC_000913_3_vch_pgi	3,815,859	Δ82 bp		[rph]–[rph]	[rph], [rph]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	= 3815858	4 (0.210)	15 (0.840)	15/270	0.3	86.4%	pseudogene (24/48 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
	?	NC_000913_3_vch_pgi	3815941 =	1 (0.060)					pseudogene (609/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

CAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTT  >  NC_000913_3_vch_pgi/3815796‑3816083                                                                                                                                                  |                                                                                                                                               tgaacccctgcttgctaagcgcaaattcaataaaccggcgctgatatgctttcatgccttcgctcctcatcttacttttctacatacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTc                                                                                                                                             <  1:244041‑M2/4‑1 (MQ=255)  taacacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTcc                                                                                                                                            >  1:46118‑M2/145‑149 (MQ=255)    aCAAAAAAAAGGCTACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                                                                                          >  1:298305/1‑149 (MQ=255)     cacctgcttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCt                                                                                                                                         >  1:241909‑M2/142‑149 (MQ=255)           cttgctaagcgcaaattcaataaactggcgctgatatggtttcatgccttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACtt                                                                                                                                   <  2:46118‑M2/14‑1 (MQ=255)                                     ggcgctgatatggtttcatgtcttgtggccccatcttagttttgtacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatc                                                                                                         <  2:69785‑M2/40‑1 (MQ=255)                                         ctaatatggtttcattccttccctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTa                                                                                                     <  1:262137‑M2/44‑1 (MQ=255)                                                           ttcgctcctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgcccgagccgccttctgcCACACTCCGGTGTTCAAGGATTCGCCCGTCTTCGGTCATCACTACGTTCATGTCGTTCTCTg                                                                                   >  1:320138‑M2/88‑149 (MQ=255)                                                                  ctcatcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCCCTGCGGCaga                                                                            >  1:34173‑M2/81‑149 (MQ=255)                                                                      tcttacttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTTCGGCAGAGTCt                                                                        >  1:139510‑M2/77‑149 (MQ=255)                                                                          acttttctacagacaaaaaaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCaa                                                                    >  1:228285‑M2/73‑149 (MQ=255)                                                                                       caaaaaaaaggcgacttctcagtcgccttaaaactcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATc                                                       <  1:66521‑M2/90‑1 (MQ=255)                                                                                            aaaaggcgactcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCaaa                                                  <  2:235843‑M2/95‑1 (MQ=255)                                                                                                      tcatcagtcgccttaaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGcc                                        >  1:246251‑M2/45‑149 (MQ=255)                                                                                                                   taaaaatcagtttgccagcgccgccttctgcCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCg                           >  1:206725‑M2/32‑149 (MQ=255)                                                                                                                        atcagtttgccagcgccgccttctgcCGTCCCCTGCGCTTCATTGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAGACCGCTTCGCGGTTGACAATTCCGACAGa                      >  1:201405‑M2/27‑149 (MQ=255)                                                                                                                                           ctttggCCGTTCCCCTCCCTTCCACGGTGCGCCCGTCTGGGGGCATCACTACGTTCAGGTCGGTCTCTGCGGCAGAGGCTTCAAAGTATTCCAGTTCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCt   <  1:310534/144‑1 (MQ=255)                                                                                                                                            ttCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGAGGCGGTGTCTTGAGCTGTTTCCATGTCGTAACCCGCTTCGCCGTTCACAATTCCGACAGAACCTGCGGCACCCCTCCCtt  >  2:208115/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                               CAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTT  >  NC_000913_3_vch_pgi/3815796‑3816083

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: ‑
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.