Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	280,453	T→C	pseudogene (283/309 nt)	yagB ←	pseudogene, CP4‑6 prophage,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	280,453	0	T	C	100.0%	250.6 / NA	65	pseudogene (283/309 nt)	yagB	pseudogene, CP4‑6 prophage,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (37/28);  total (37/28)

ACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACTGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAGTT  >  NC_000913/280319‑280587                                                                                                                                       |                                                                                                                                       aCTGCTTCAGTCTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGccc                                                                                                                                    <  1:787799/139‑1 (MQ=255)                       cGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCa                                                                                                              >  1:429484/1‑139 (MQ=255)                         ggATAACGCTTACCGCTCATGGGCACCTCTC‑TTAAGCCATTTTAGATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGcc                                                                                                           <  1:1040066/139‑1 (MQ=255)                          gATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGcc                                                                                                           <  2:958840/139‑1 (MQ=255)                               cGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTa                                                                                                      >  2:87313/1‑139 (MQ=255)                                    aCCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 <  2:949030/139‑1 (MQ=255)                                    aCCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 <  1:500444/139‑1 (MQ=255)                                        cTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 >  1:1009408/1‑135 (MQ=255)                                        cTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 <  2:1009408/135‑1 (MQ=255)                                                                aTTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGcgcg                                                                              >  1:135004/1‑130 (MQ=255)                                                                aTTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGcgcg                                                                              <  2:135004/130‑1 (MQ=255)                                                                 ttttAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGAt                                                                    >  1:1116198/1‑139 (MQ=255)                                                                 ttttAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGAt                                                                    >  1:344509/1‑139 (MQ=255)                                                                                     tCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGagcagc                                                >  2:94152/1‑139 (MQ=255)                                                                                        gTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGTCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATc                                             <  2:135463/139‑1 (MQ=255)                                                                                         ttAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 <  1:967935/86‑1 (MQ=255)                                                                                         ttAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 >  2:967935/1‑86 (MQ=255)                                                                                          tAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTa                                                                                                                              >  2:666677/1‑56 (MQ=255)                                                                                          tAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTa                                                                                                                              <  1:666677/56‑1 (MQ=255)                                                                                          tAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAg                                           >  2:1084004/1‑139 (MQ=255)                                                                                                 gTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGcc                                                                                                           <  1:362505/68‑1 (MQ=255)                                                                                                 gTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGcc                                                                                                           >  2:362505/1‑68 (MQ=255)                                                                                                 gTGGCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGa                                    >  1:161158/1‑139 (MQ=255)                                                                                                   ggCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTa                                                                                                                              >  2:278968/1‑47 (MQ=255)                                                                                                   ggCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTa                                                                                                                              <  1:278968/47‑1 (MQ=255)                                                                                                   ggCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGAtt                                                                   <  2:761609/106‑1 (MQ=255)                                                                                                   ggCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGAtt                                                                   >  1:761609/1‑106 (MQ=255)                                                                                                   ggCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGAtg                                  >  2:927207/1‑139 (MQ=255)                                                                                                   ggCGATTCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGAtg                                  >  1:228732/1‑139 (MQ=255)                                                                                                         tCAAAATTGCGATATATACATACCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGAc                            <  2:619205/139‑1 (MQ=255)                                                                                                                              acCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACa                                                                                               >  1:886907/1‑51 (MQ=255)                                                                                                                              acCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACa                                                                                               <  2:886907/51‑1 (MQ=255)                                                                                                                              acCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGt                                                                             <  1:375700/69‑1 (MQ=255)                                                                                                                              acCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGt                                                                             >  2:375700/1‑69 (MQ=255)                                                                                                                              acCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCggg                  >  2:835529/1‑128 (MQ=255)                                                                                                                              acCCATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCggg                  <  1:835529/128‑1 (MQ=255)                                                                                                                               cccATGACCGCCCAGCGTATCGGCTTCACCAGTCAGcc                                                                                                           <  1:712181/38‑1 (MQ=255)                                                                                                                               cccATGACCGCCCAGCGTATCGGCTTCACCAGTCAGcc                                                                                                           >  2:712181/1‑38 (MQ=255)                                                                                                                               cccATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTgcg                                                                                <  2:709196/65‑1 (MQ=255)                                                                                                                               cccATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTgcg                                                                                >  1:709196/1‑65 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 >  1:909634/1‑46 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 <  2:909634/46‑1 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGacac                                                                                      <  2:244118/57‑1 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGacac                                                                                      >  2:413948/1‑57 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGacac                                                                                      <  1:413948/57‑1 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGacac                                                                                      >  1:244118/1‑57 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGcgcg                                                                              >  2:1159976/1‑65 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGcgcg                                                                              <  1:1159976/65‑1 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAg    >  2:799275/1‑139 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAg    >  1:1162259/1‑139 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAg    >  1:161194/1‑139 (MQ=255)                                                                                                                                 cATGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAg    >  1:725983/1‑139 (MQ=255)                                                                                                                                  aTGACCGCCCAGCGTATCGGCTTCACCAGTCAGcc                                                                                                           <  2:78209/35‑1 (MQ=255)                                                                                                                                  aTGACCGCCCAGCGTATCGGCTTCACCAGTCAGcc                                                                                                           >  1:78209/1‑35 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 >  1:1160695/1‑44 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 <  2:366318/44‑1 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 <  2:1160695/44‑1 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTa                                                                                                 >  1:366318/1‑44 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGaca                                                                                       >  2:558198/1‑54 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGaca                                                                                       <  1:558198/54‑1 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCTCAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAGtt  >  2:441269/1‑139 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCt            <  1:413055/129‑1 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCt            >  2:413055/1‑129 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAGtt  >  1:325929/1‑139 (MQ=255)                                                                                                                                   tGACCGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAGtt  >  1:1133698/1‑139 (MQ=255)                                                                                                                                       |                                                                                                                                       ACTGCTTCAGTTTTAAACTCTTCGGGATAACGCTTACCGCTCATGGGCACCTCTCTTTAAGCCATTTTAAATGACTCGGAGGTGTCTGTTAAACCCGTGGCGATTCAAAATTGCGATATATACATACCCATGACTGCCCAGCGTATCGGCTTCACCAGTCAGCCCGTTACGGTACAGTGTGACACAGTGCGCGTACCTGGGATTCAGCTCACAGGAGAGCAGCATCAGCTCCAGATGTGCGACAAAATGCGGGAAGGCTTCATCCAGTT  >  NC_000913/280319‑280587

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑