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%	127.9 / NA	40	pseudogene (40/678 nt)	yedN	pseudogene, IpaH/YopM family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/21);  total (19/21)

CATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCAAT  >  NC_000913/2011869‑2012133                                                                                                                                     |                                                                                                                                     caTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAttt                                                                                                                                >  2:37515/1‑139 (MQ=255) aaTTTTTTTTGTAGTCATCCGATGCTCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAGAGTCTCGAATCTGTATTCTTCGTAAAGTAGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAAttt                                                                                                                                >  1:214510/2‑139 (MQ=255)  aTTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa                                                                                                                               <  1:37515/139‑1 (MQ=255)            aaGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtgg                                                                                                                     <  2:854686/139‑1 (MQ=255)                cATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa                                                                                                                               <  2:546897/125‑1 (MQ=255)                cATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTa                                                                                                                               >  1:546897/1‑125 (MQ=255)                            cttcttTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAg                                                                                                         >  2:243605/1‑135 (MQ=255)                            cttcttTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAg                                                                                                         <  1:243605/135‑1 (MQ=255)                                        aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt                                                                                         >  1:1186887/1‑139 (MQ=255)                                        aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt                                                                                         >  1:504188/1‑139 (MQ=255)                                        aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt                                                                                         >  1:7215/1‑139 (MQ=255)                                          ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAGCTTTAATTTATGCCGAAtggg                                                                                                                    >  2:773688/1‑110 (MQ=255)                                          ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                    <  1:773688/110‑1 (MQ=255)                                          ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt                                                                                       >  1:853454/1‑139 (MQ=255)                                          ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt                                                                                       <  2:341374/139‑1 (MQ=255)                                                cAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTCTCATGAt                                                                                 <  2:504188/139‑1 (MQ=255)                                                  gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                    <  1:919638/102‑1 (MQ=255)                                                  gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                    >  2:919638/1‑102 (MQ=255)                                                  gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt                                                                                                               >  2:1083690/1‑107 (MQ=255)                                                  gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATgggtgggt                                                                                                               <  1:1083690/107‑1 (MQ=255)                                                  gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATaa                                                                               >  2:1004753/1‑139 (MQ=255)                                                     gCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAc                                                                            <  2:1186887/139‑1 (MQ=255)                                                     gCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAc                                                                            <  2:7215/139‑1 (MQ=255)                                                      cTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc                                                                           <  2:853454/139‑1 (MQ=255)                                                                        cTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc                                                                           >  2:865565/1‑121 (MQ=255)                                                                        cTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc                                                                           <  1:865565/121‑1 (MQ=255)                                                                          ggAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                    <  2:1119891/78‑1 (MQ=255)                                                                          ggAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                                                    >  1:1119891/1‑78 (MQ=255)                                                                                 gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGAt                                                                                                <  2:1138371/91‑1 (MQ=255)                                                                                 gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGAt                                                                                                >  1:1138371/1‑91 (MQ=255)                                                                                 gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTg                                                >  2:505294/1‑139 (MQ=255)                                                                                          gTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc                                                                       <  1:489502/107‑1 (MQ=255)                                                                                          gTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc                                                                       >  2:489502/1‑107 (MQ=255)                                                                                           tAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAgaga                                      <  1:505294/139‑1 (MQ=255)                                                                                                             ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCa                                          >  2:912754/1‑117 (MQ=255)                                                                                                             ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCa                                          <  1:912754/117‑1 (MQ=255)                                                                                                                cAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCag                                         <  1:1129560/115‑1 (MQ=255)                                                                                                                cAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCag                                         >  2:1129560/1‑115 (MQ=255)                                                                                                                      tAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCt           <  1:1004753/139‑1 (MQ=255)                                                                                                                               taAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCAAt  <  1:283803/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                     CATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCATTCGAAATATTCTGAGTGCAAT  >  NC_000913/2011869‑2012133

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: ‑