Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,525,805	A→G	pseudogene (1198/1241 nt)	yjhR →	helicase YjhR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,525,805	0	A	G	100.0%	145.0 / NA	42	pseudogene (1198/1241 nt)	yjhR	helicase YjhR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (17/25);  total (17/25)

CTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGAAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAA  >  NZ_CP009273/4525725‑4525882                                                                                 |                                                                              cTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc                                                                      <  1:186738/90‑1 (MQ=255)   ggTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCaa                                                                    <  2:218918/90‑1 (MQ=255)   ggTTCAGTGCTACACGGGAAGATAAATATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCaa                                                                    <  1:207740/90‑1 (MQ=255)    gTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAat                                                                   >  2:171041/1‑90 (MQ=255)    gTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAat                                                                   >  1:121218/1‑90 (MQ=255)    gTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAat                                                                   >  1:228031/1‑90 (MQ=255)     ttCAGCGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAata                                                                  <  1:259543/90‑1 (MQ=255)          tGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATgg                                                             <  2:355872/90‑1 (MQ=255)          tGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATgg                                                             <  1:167829/90‑1 (MQ=255)           gCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGt                                                            <  2:20726/90‑1 (MQ=255)              acacGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGt                                                         >  1:267461/1‑90 (MQ=255)                   ggAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc                                                                      >  2:339097/1‑72 (MQ=255)                   ggAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc                                                                      <  1:339097/72‑1 (MQ=255)                   ggAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGa                                                    >  2:349177/1‑90 (MQ=255)                   ggAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGa                                                    >  2:253531/1‑90 (MQ=255)                      aGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCa                                                 >  1:250264/1‑90 (MQ=255)                                 aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc                                                                      >  1:236089/1‑58 (MQ=255)                                 aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc                                                                      >  1:282016/1‑58 (MQ=255)                                 aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc                                                                      <  2:282016/58‑1 (MQ=255)                                 aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc                                                                      <  2:236089/58‑1 (MQ=255)                                 aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCa                                           >  1:373415/1‑85 (MQ=255)                                 aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCa                                           <  2:373415/85‑1 (MQ=255)                                 aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCttt                                      >  2:97828/1‑90 (MQ=255)                                    gatacgatacGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTaaa                                   <  2:183364/90‑1 (MQ=255)                                    gatacgatacGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTaaa                                   <  1:271116/90‑1 (MQ=255)                                             cgTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAata                                                                  >  2:357919/1‑50 (MQ=255)                                             cgTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAata                                                                  <  1:357919/50‑1 (MQ=255)                                              gTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGc                         <  1:256126/90‑1 (MQ=255)                                               tCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGcc                        >  2:392727/1‑90 (MQ=255)                                                   tGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTc                    <  2:250264/90‑1 (MQ=255)                                                   tGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTc                    <  1:226796/90‑1 (MQ=255)                                                     gtgtACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCAt                  <  1:349177/90‑1 (MQ=255)                                                          ccGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATAc             <  2:129667/90‑1 (MQ=255)                                                           cGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACa            <  1:67859/90‑1 (MQ=255)                                                           cGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACa            <  2:45409/90‑1 (MQ=255)                                                           cGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACa            <  2:75803/90‑1 (MQ=255)                                                             tggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAgg          <  1:227372/90‑1 (MQ=255)                                                             tggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAgg          <  1:21695/90‑1 (MQ=255)                                                              ggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGa         >  1:336793/1‑90 (MQ=255)                                                              ggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGa         >  2:362700/1‑90 (MQ=255)                                                              ggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGa         >  2:44290/1‑90 (MQ=255)                                                                     gCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTaa  <  1:97828/90‑1 (MQ=255)                                                                                 |                                                                              CTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGAAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAA  >  NZ_CP009273/4525725‑4525882

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑