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%	117.7 / NA	39	pseudogene (40/678 nt)	yedN	pseudogene, IpaH/YopM family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (17/22);  total (17/22)

TCCACATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCAT  >  NC_000913/2011865‑2012112                                                                                                                                         |                                                                                                                tCCACATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCATTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTa                                                                                                               >  1:1232840/1‑139 (MQ=255)         ttttttGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGc                                                                                                       <  1:715026/139‑1 (MQ=255)          tttttGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCGAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGcc                                                                                                      <  2:1232840/139‑1 (MQ=255)                 aGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                               <  1:1057234/139‑1 (MQ=255)                             cgcCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGt                                                                                   >  2:1052968/1‑139 (MQ=255)                                     tttACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGAt                                                                           >  1:883858/1‑139 (MQ=255)                                            aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGaa                                                                                                   <  2:1117046/108‑1 (MQ=255)                                            aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGaa                                                                                                   >  1:1117046/1‑108 (MQ=255)                                            aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt                                                                    >  1:701922/1‑139 (MQ=255)                                            aaTTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCt                                                                    >  1:909543/1‑139 (MQ=255)                                              ttAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTAt                                                                  >  2:188216/1‑139 (MQ=255)                                               tAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATc                                                                 <  2:909543/139‑1 (MQ=255)                                               tAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATc                                                                 <  2:883858/139‑1 (MQ=255)                                                    cAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGAt                                                            <  1:1058733/139‑1 (MQ=255)                                                      gTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATaa                                                          <  2:332098/139‑1 (MQ=255)                                                            gAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtgggtggg                                                                                           >  2:702118/1‑100 (MQ=255)                                                            gAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtgggtggg                                                                                           <  1:702118/100‑1 (MQ=255)                                                            gAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc                                                      <  1:503067/137‑1 (MQ=255)                                                            gAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAAcc                                                      >  2:503067/1‑137 (MQ=255)                                                              ataacagacagaGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCAATCATGATAAAACCTATc                                                  <  1:852839/128‑1 (MQ=255)                                                              aaCCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATc                                                  <  1:492736/139‑1 (MQ=255)                                                                     gCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGAt                                                            >  2:403833/1‑122 (MQ=255)                                                                     gCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGAt                                                            <  1:403833/122‑1 (MQ=255)                                                                            cTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCga                                    >  2:855075/1‑139 (MQ=255)                                                                                    tGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTCAATTTATGCCGAATGGGTGGGTTACCAGTGCCCTGATTTTTTCTATCATGATAAAACCTAGCTTATTATAAATctgtctcttat                            >  2:852839/1‑129 (MQ=255)                                                                                     gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                               <  1:4448/71‑1 (MQ=255)                                                                                     gTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAAtggg                                                                                               >  2:4448/1‑71 (MQ=255)                                                                                           ttCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCa                     <  2:868920/139‑1 (MQ=255)                                                                                            tCGTAAAGTCGTCTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAACTCGAGAAATCTTGAAACCag                    <  2:760630/139‑1 (MQ=255)                                                                                                        cTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAAcc                      <  2:111457/125‑1 (MQ=255)                                                                                                        cTAGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAAcc                      >  1:111457/1‑125 (MQ=255)                                                                                                          aGAAACTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCAcc      <  2:96210/139‑1 (MQ=255)                                                                                                              aCTCTGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCAt  <  2:1274333/139‑1 (MQ=255)                                                                                                                 ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATa                                                           >  2:1048407/1‑79 (MQ=255)                                                                                                                 ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATa                                                           <  1:1048407/79‑1 (MQ=255)                                                                                                                 ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCAt  <  1:1015597/136‑1 (MQ=255)                                                                                                                 ctGCAATATTAGTCGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCAt  >  2:1015597/1‑136 (MQ=255)                                                                                                                              cGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCAc       >  2:1239992/1‑118 (MQ=255)                                                                                                                              cGATATAAACTTTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCAc       <  1:1239992/118‑1 (MQ=255)                                                                                                                                         |                                                                                                                TCCACATTTTTTTTGAAGTCATTCGATGCGCCTTCTTTTACTGAATTAGCCCAGTCGCTGAAACCTTTGCAAAGTCTGGAATCTGTAATTTTCGTAAAGTTGTCTAGAAACTCTGCAATATTAGTCGATATAAACTCTAATTTATGCCGAATGGGTGGGTTACCAGTTCCCTGATTTTTTCTATCATGATAAAACCTATCTTATTATAAATCGAGAAATCTTGAAACCAGAGACTATAATCACCCCAT  >  NC_000913/2011865‑2012112

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑