Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,783,249	T→C	pseudogene (56/240 nt)	pinH ←	pseudogene, invertase resolvase family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,783,249	0	T	C	100.0%	178.8 / NA	50	pseudogene (56/240 nt)	pinH	pseudogene, invertase resolvase family
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/25);  total (25/25)

TCCCCCCATTGTTGGGCAAATATAGATTGGGCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGTTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTAACGCTGTTATTG  >  NC_000913/2783114‑2783374                                                                                                                                        |                                                                                                                              tCCCCCCATTGTTGGGCAAATATAGATTGGGCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTcc                                                                                                                            <  2:51652/139‑1 (MQ=255)     cccATTGTTGGGCAAATATAGATTGGGCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGc                                                                                                                        <  2:103320/139‑1 (MQ=255)            ttgGGCAAATATAGATTGGGCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCgatgat                                                                                                                 >  1:650935/1‑139 (MQ=255)               ggCAAATATAGATTGTGCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTc                                                                                                              >  2:448385/1‑139 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCg                                                                                                                      <  1:173323/116‑1 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCg                                                                                                                      >  2:173323/1‑116 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGa                                                                                                          <  2:917540/128‑1 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGa                                                                                                          >  1:917540/1‑128 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTc                                                                                               >  2:32580/1‑139 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTc                                                                                               >  1:789549/1‑139 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTc                                                                                               >  1:500404/1‑139 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTc                                                                                               >  1:337815/1‑139 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTc                                                                                               >  1:301991/1‑139 (MQ=255)                              ggCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTc                                                                                               >  2:833094/1‑139 (MQ=255)                                                aaTACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCa                                                                             <  2:301991/139‑1 (MQ=255)                                                 aTACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCAc                                                                            >  1:493137/1‑139 (MQ=255)                                                     cACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGtttttt                                                                                                <  1:607349/115‑1 (MQ=255)                                                     cACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGtttttt                                                                                                >  2:607349/1‑115 (MQ=255)                                                     cACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGtt                                                                        >  1:547838/1‑139 (MQ=255)                                                       cGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGAcc                                                                                                        <  2:590788/105‑1 (MQ=255)                                                       cGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGAcc                                                                                                        >  1:590788/1‑105 (MQ=255)                                                       cGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGtttt                                                                      >  1:25422/1‑139 (MQ=255)                                                              acaGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGa                                                               <  2:547838/139‑1 (MQ=255)                                                              acaGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGa                                                               <  2:500404/139‑1 (MQ=255)                                                                    cctccAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGt                                                         <  2:559088/139‑1 (MQ=255)                                                                               aCGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGAcct                                                                                    >  2:693268/1‑101 (MQ=255)                                                                               aCGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGAcct                                                                                    <  1:693268/101‑1 (MQ=255)                                                                                 gACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACg                                            <  2:810842/139‑1 (MQ=255)                                                                                 gACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACg                                            <  2:343254/139‑1 (MQ=255)                                                                                 gACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACg                                            <  2:337815/139‑1 (MQ=255)                                                                                             caTACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTtcagt                                <  1:197964/139‑1 (MQ=255)                                                                                             caTACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTtcagt                                <  1:448385/139‑1 (MQ=255)                                                                                                    cgcCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGa                                                               <  2:647953/101‑1 (MQ=255)                                                                                                    cgcCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGa                                                               >  1:647953/1‑101 (MQ=255)                                                                                                    cgcCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCNGTTCTTCAGTCAGGCgt                         >  1:34836/1‑139 (MQ=255)                                                                                                       cccAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCgtggt                      >  2:530132/1‑139 (MQ=255)                                                                                                         cAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGa                                                                                                          <  2:370375/53‑1 (MQ=255)                                                                                                         cAGTCGGTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGa                                                                                                          >  1:370375/1‑53 (MQ=255)                                                                                                               gTTCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTa              >  1:97723/1‑139 (MQ=255)                                                                                                                ttCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTaa             >  1:281378/1‑139 (MQ=255)                                                                                                                 tCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTAAc            <  1:239134/139‑1 (MQ=255)                                                                                                                 tCAGTTTACAGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTAAc            <  2:493137/139‑1 (MQ=255)                                                                                                                          aGACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTAACGCTGTTAtt   <  2:25422/139‑1 (MQ=255)                                                                                                                           gACTAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTAACGCTGTTATTg  <  2:97723/139‑1 (MQ=255)                                                                                                                              tAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCgtg                        <  1:315636/114‑1 (MQ=255)                                                                                                                              tAGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCgtg                        >  2:315636/1‑114 (MQ=255)                                                                                                                               aGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACg                                                                   <  2:20492/70‑1 (MQ=255)                                                                                                                               aGCAGTGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACg                                                                   >  1:20492/1‑70 (MQ=255)                                                                                                                                    tGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTAACGCTGTTa     <  1:756739/127‑1 (MQ=255)                                                                                                                                    tGCGCTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTAACGCTGTTa     >  2:756739/1‑127 (MQ=255)                                                                                                                                        |                                                                                                                              TCCCCCCATTGTTGGGCAAATATAGATTGGGCCAGAGCACGAAAGTTAATACCACGTTCGCACAGCTCCTCCAACAGCACGACAAGATGCCACATACTGCGCCCCAGTCGGTTCAGTTTACAGACTAGCAGTGCGTTCCCTGCCGATGATGTCCTGACCAGTTTTTTCAGTCCGGACCTCCTGCCACGGTTTTACGTTGAAGTGGTAACCCTGAGCACGCAGTTCTTCAGTCAGGCGTGGTGCACCGTAACGCTGTTATTG  >  NC_000913/2783114‑2783374

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑