Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,777,187	T→C	pseudogene (1184/1374 nt)	BW25113_RS25705 ←	DUF5507 domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,777,187	0	T	C	100.0%	137.7 / NA	38	pseudogene (1184/1374 nt)	BW25113_RS25705	DUF5507 domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (21/17);  total (21/17)

AACGGGATCATCCTCAGAGGAACTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTTCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCATAGTTACTGAAGTTCT  >  NZ_CP009273/2777057‑2777316                                                                                                                                   |                                                                                                                                  aaCGGGATCATCCTCAGAGGAACTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTcac                                                                                                                            <  2:124526/138‑1 (MQ=255) aaCGGGATCATCCTCAGAGGAACTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTca                                                                                                                             >  1:129819/1‑137 (MQ=255)                agagGAACTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGAtttt                                                                                                            >  1:623179/1‑139 (MQ=255)                    gAACTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCAt                                                                                                        <  2:178969/139‑1 (MQ=255)                       cTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGCGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCAt                                                                                                        >  2:146918/1‑136 (MQ=255)                       cTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCAt                                                                                                        <  1:146918/136‑1 (MQ=255)                       cTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTa                                                                                                      >  1:513343/1‑138 (MQ=255)                       cTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTa                                                                                                      <  2:513343/138‑1 (MQ=255)                          tcatcaAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTActct                                                                                                  <  1:572508/139‑1 (MQ=255)                          tcatcaAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTActct                                                                                                  >  1:595445/1‑139 (MQ=255)                          tcatcaAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTActct                                                                                                  >  1:73182/1‑139 (MQ=255)                          tcatcaAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTActc                                                                                                   <  1:571655/138‑1 (MQ=255)                               aaaGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCttgtt                                                                                              <  1:309552/138‑1 (MQ=255)                                  gTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCttg                                                                                                <  2:295054/133‑1 (MQ=255)                                  gTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCttg                                                                                                >  1:295054/1‑133 (MQ=255)                                        atcCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAgg                                                                                     <  2:129819/138‑1 (MQ=255)                                            ataaataaAATATCATCGAATGGTGCCACGCCCGTGATGGGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCAt                                                                                <  1:312300/139‑1 (MQ=255)                                                    aataTCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGAttttt                                                                                                           >  1:233237/1‑104 (MQ=255)                                                    aataTCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGAttttt                                                                                                           <  2:233237/104‑1 (MQ=255)                                                      tatCATCTAATGATACCACGCCCGTTATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATaca                                                                      <  2:73182/139‑1 (MQ=255)                                                           tcGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTActc                                                                                                   >  1:64966/1‑105 (MQ=255)                                                           tcGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTActc                                                                                                   <  2:64966/105‑1 (MQ=255)                                                                             gTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAAt                                                >  2:314090/1‑138 (MQ=255)                                                                                atgaGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACg                                            <  2:220556/139‑1 (MQ=255)                                                                                               ttattaCGATCAGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTcaca                              >  1:220127/1‑138 (MQ=255)                                                                                                          aGTCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATc                   <  2:623179/138‑1 (MQ=255)                                                                                                            tCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACg                                                                    <  1:46314/87‑1 (MQ=255)                                                                                                            tCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACg                                                                    >  2:46314/1‑87 (MQ=255)                                                                                                            tCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCa                  >  1:385611/1‑137 (MQ=255)                                                                                                            tCAATACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCa                  >  1:343456/1‑137 (MQ=255)                                                                                                                tACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCATAGTTa            >  1:487618/1‑139 (MQ=255)                                                                                                                tACTCCACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCATAGTTa            >  2:517632/1‑139 (MQ=255)                                                                                                                     cACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCATAGTTACTg         >  2:377246/1‑137 (MQ=255)                                                                                                                     cACTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCATAGTTACTg         >  2:446646/1‑137 (MQ=255)                                                                                                                      aCTTAAACCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCATAGTTACTGAAg      >  1:262194/1‑139 (MQ=255)                                                                                                                          aaaCCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAgg                                                                                     <  1:124487/56‑1 (MQ=255)                                                                                                                          aaaCCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAgg                                                                                     >  2:124487/1‑56 (MQ=255)                                                                                                                          aaaCCGTTTCCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCATAGTTACTGAAGTTCt  >  1:583367/1‑139 (MQ=255)                                                                                                                                   |                                                                                                                                  AACGGGATCATCCTCAGAGGAACTATCATCAAAGTCATCATCCATAAATAAAATATCATCGAATGGTGCCACGCCCGTGATGAGTTTTATTTTATTATTACGATCAGTCAATACTCCACTTAAACCGTTTTCGCTCACAGGTTTTAATGATTTTTCATTACTCTTGTTGTAAGCAGGCGCATTAAAAATACACGGAGTATCAACATCAAACAATGACGTTCCCCAGTTCACATATTGAATATCATAGTTACTGAAGTTCT  >  NZ_CP009273/2777057‑2777316

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑