Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,012,001	C→T	pseudogene (40/678 nt)	yedN ←	pseudogene, IpaH/YopM family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,012,001	0	C	T	100.0%	150.3 / NA	48	pseudogene (40/678 nt)	yedN	pseudogene, IpaH/YopM family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (24/24);  total (24/24)

ACATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCA  >  NC_000913/2011868‑2012131                                                                                                                                      |                                                                                                                                   acaTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAtt                                                                                                                               >  1:1827609/1‑139 (MQ=255) acaTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAAATAGCCCAGTCGCTGAAACCTTGGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAtt                                                                                                                               >  1:496297/1‑139 (MQ=255)   aTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa                                                                                                                             >  2:1117586/1‑139 (MQ=255)       tttttGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGcc                                                                                                                         <  2:1827609/139‑1 (MQ=255)         tttGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAt                                                                                                                                <  2:1000410/130‑1 (MQ=255)         tttGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAt                                                                                                                                >  1:1000410/1‑130 (MQ=255)              aGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                  <  2:1577287/139‑1 (MQ=255)                   ttCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt                                                                                                             <  1:1117586/139‑1 (MQ=255)                   ttCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt                                                                                                             <  1:442732/139‑1 (MQ=255)                             cttcttTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                  <  1:1218242/124‑1 (MQ=255)                             cttcttTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                  >  2:1218242/1‑124 (MQ=255)                                     aCTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGAtttt                                                                                           >  2:127646/1‑139 (MQ=255)                                       tGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                  >  1:101556/1‑114 (MQ=255)                                       tGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                  <  2:101556/114‑1 (MQ=255)                                         aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTGGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATg                                                                                                                           >  1:1198686/1‑103 (MQ=255)                                         aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATg                                                                                                                           <  2:1198686/103‑1 (MQ=255)                                         aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt                                                                                       >  2:280399/1‑139 (MQ=255)                                           ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt                                                                                     <  1:453821/139‑1 (MQ=255)                                           ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt                                                                                     <  1:280399/139‑1 (MQ=255)                                              gCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt                                                                                     >  1:587069/1‑136 (MQ=255)                                              gCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt                                                                                     <  2:587069/136‑1 (MQ=255)                                                  aGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATa                                                                              <  1:127646/139‑1 (MQ=255)                                                   gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCa                                                                                                        <  2:1828337/112‑1 (MQ=255)                                                   gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCa                                                                                                        >  1:1828337/1‑112 (MQ=255)                                                   gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATc                                                                                    >  1:1093078/1‑132 (MQ=255)                                                   gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATc                                                                                    <  2:1093078/132‑1 (MQ=255)                                                   gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGa                                                                                >  1:366920/1‑136 (MQ=255)                                                   gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGa                                                                                <  2:366920/136‑1 (MQ=255)                                                      gCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAc                                                                          <  1:951379/139‑1 (MQ=255)                                                                 tGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCt                                                                    <  2:1115598/134‑1 (MQ=255)                                                                 tGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCt                                                                    >  1:1115598/1‑134 (MQ=255)                                                                        tCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTg                                                                                                >  2:469114/1‑99 (MQ=255)                                                                        tCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATGAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTg                                                                                                <  1:469114/99‑1 (MQ=255)                                                                                  gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTg                                              >  2:941100/1‑139 (MQ=255)                                                                                       tttCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAAcc                                         <  2:1528144/139‑1 (MQ=255)                                                                                           gTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCagag                                     <  2:1780084/139‑1 (MQ=255)                                                                                                           aCTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt                                                                                                             <  1:1267589/51‑1 (MQ=255)                                                                                                           aCTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt                                                                                                             >  2:1267589/1‑51 (MQ=255)                                                                                                              ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCg                  >  2:1799120/1‑139 (MQ=255)                                                                                                                gCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATc                                                                                    <  1:786818/71‑1 (MQ=255)                                                                                                                gCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATc                                                                                    >  2:786818/1‑71 (MQ=255)                                                                                                                    tatTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAatat            >  1:328498/1‑139 (MQ=255)                                                                                                                      ttAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCgag                                                      <  1:723840/95‑1 (MQ=255)                                                                                                                      ttAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCgag                                                      >  2:723840/1‑95 (MQ=255)                                                                                                                           cGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGt     >  1:646781/1‑139 (MQ=255)                                                                                                                              tataAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc                                                                     <  2:939981/72‑1 (MQ=255)                                                                                                                              tataAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc                                                                     >  1:939981/1‑72 (MQ=255)                                                                                                                              tataAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCa  >  1:1505736/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                   ACATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCA  >  NC_000913/2011868‑2012131

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: ‑