Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,565,565	G→A	pseudogene (1830/2937 nt)	BW25113_RS22615 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,565,565	0	G	A	100.0%	155.3 / NA	40	pseudogene (1830/2937 nt)	BW25113_RS22615	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/18);  total (22/18)

CGAAAGAGCATATGACTTTTTCTTTAATCACGGATGCCTGGATTTGCCCGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTGGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAGCCATGATC  >  NZ_CP009273/4565432‑4565686                                                                                                                                      |                                                                                                                          cGAAAGAGCATATGACTTTTTCTTTAATCACGGATGACTGGATTTGCCCGGTAACCAATAAAATCCTGGATACGGCTTGTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAgcgc                                                                                                                       >  2:291924/1‑138 (MQ=255)       agCATATGACTTTTTCTTTAATCACGGATGCCTGGATTTGCCCGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGa                                                                                                                <  1:45656/139‑1 (MQ=255)                                     ccTGGATTTGCCCGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCTGAAAGTCACAATGcc                                                                                  >  2:759144/1‑139 (MQ=255)                                         gATTTGCCCGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGaa                                                                              <  1:263624/139‑1 (MQ=255)                                              gCCCGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTg                                                                         >  1:489650/1‑139 (MQ=255)                                              gCCCGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACGTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCt                                                                          <  2:328142/138‑1 (MQ=255)                                              gCCCGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCCTATCTGCCTACCCATATTTAGTTCGAGCATCTTATCCTAGCGCAATATGACACTTTTGTCGCGTAGAAAGACACAATGCCGGAAATCTg                                                                         >  2:202978/1‑139 (MQ=255)                                               cccGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCt                                                                          >  2:335529/1‑137 (MQ=255)                                               cccGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCt                                                                          <  1:335529/137‑1 (MQ=255)                                                    tAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCt                                                                   >  1:533389/1‑139 (MQ=255)                                                       ccAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGa                                                                >  2:3552/1‑139 (MQ=255)                                                       ccAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGa                                                                <  1:3552/139‑1 (MQ=255)                                                             aaaTCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGtt                                                           <  1:459223/138‑1 (MQ=255)                                                             aaaTCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGtt                                                           <  2:636377/138‑1 (MQ=255)                                                             aaaTCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGtt                                                           <  2:141338/138‑1 (MQ=255)                                                                tCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTca                                                         >  2:266979/1‑137 (MQ=255)                                                                   tGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAgg                                                     >  1:148449/1‑138 (MQ=255)                                                                     gATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAgg                                                     >  2:171190/1‑136 (MQ=255)                                                                                               ttATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCa                        >  2:700059/1‑139 (MQ=255)                                                                                               ttATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCa                        >  2:141237/1‑139 (MQ=255)                                                                                                 aTCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCAc                       <  1:141237/138‑1 (MQ=255)                                                                                                    tGCCTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGa                   >  1:664061/1‑139 (MQ=255)                                                                                                      ccTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCTGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGAc                  <  1:759144/138‑1 (MQ=255)                                                                                                      ccTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGAc                  <  2:329695/138‑1 (MQ=255)                                                                                                      ccTACCCATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACt                 >  2:320537/1‑139 (MQ=255)                                                                                                          cccATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGt             <  1:383918/139‑1 (MQ=255)                                                                                                          cccATATTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGt             <  1:305105/139‑1 (MQ=255)                                                                                                             atatTTCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAg          <  2:148449/139‑1 (MQ=255)                                                                                                                tttCGTTCGAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAGcc        <  2:489650/138‑1 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCa                        <  1:761245/117‑1 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCa                        >  2:761245/1‑117 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGt             >  2:442130/1‑128 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGt             <  1:442130/128‑1 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAGCCATGATc  >  2:102880/1‑139 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAGCCATGATc  >  1:110216/1‑139 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAGCCATGATc  >  1:561470/1‑139 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAGCCATGATc  >  1:437915/1‑139 (MQ=255)                                                                                                                     ttcgAGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGAAAGTAACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAGCCATGATc  >  1:431775/1‑139 (MQ=255)                                                                                                                         aGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGa                                                                                               <  2:125545/42‑1 (MQ=255)                                                                                                                         aGCATCTTACCCTAGCGCAATATGACACTTTTGTCGCGCAGa                                                                                               >  1:125545/1‑42 (MQ=255)                                                                                                                                      |                                                                                                                          CGAAAGAGCATATGACTTTTTCTTTAATCACGGATGCCTGGATTTGCCCGGTAACCAATAAAATCCTGGATACGGCTTTTAAAGGCTTAACCCCTTATCTGCCTACCCATATTTCGTTCGAGCATCTTACCCTGGCGCAATATGACACTTTTGTCGCGCAGAAAGTCACAATGCCGGAAATCTGGAAGCTGGATCGTTCACAGGAAGACTACGCAGAGGGTCTGGCAAAAGCACGCGACTGGGTCAGCCATGATC  >  NZ_CP009273/4565432‑4565686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑