Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,082,060	A→G	pseudogene (601/726 nt)	efeU →	ferrous iron permease (pseudogene)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,082,060	0	A	G	100.0%	203.8 / NA	56	pseudogene (601/726 nt)	efeU	ferrous iron permease (pseudogene)
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (29/27);  total (29/27)

CCGCAGGGCTGGCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGATTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCCGCGTAACAAA  >  NC_000913/1081929‑1082189                                                                                                                                    |                                                                                                                                  ccgcAGGGCTGGCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTgg                                                                                                                            <  1:1489230/139‑1 (MQ=255)          tGGCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGa                                                                                                                   <  1:140183/139‑1 (MQ=255)            gCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAg                                                                                                                 >  2:1065583/1‑139 (MQ=255)            gCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAg                                                                                                                 >  2:1252761/1‑139 (MQ=255)                 tGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAgcgc                                                                                                              >  2:1583375/1‑137 (MQ=255)                 tGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAgcgc                                                                                                              <  1:1583375/137‑1 (MQ=255)                 tGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCg                                                                                                            >  1:1480772/1‑139 (MQ=255)                   gTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTgg                                                                                                                            >  2:1169061/1‑121 (MQ=255)                   gTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTgg                                                                                                                            <  1:1169061/121‑1 (MQ=255)                   gTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAg                                                                                                          >  2:200539/1‑139 (MQ=255)                                   tCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGcc                                                                                          <  2:1480772/139‑1 (MQ=255)                                     aTGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGACGGGGTTTTTGTCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGt                                                                                        <  1:1077747/139‑1 (MQ=255)                                         aGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTgg                                                                                    <  1:1252761/139‑1 (MQ=255)                                          gCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   <  1:725392/139‑1 (MQ=255)                                            cGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   <  1:215224/137‑1 (MQ=255)                                            cGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   >  2:215224/1‑137 (MQ=255)                                                   tgGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   >  1:604583/1‑130 (MQ=255)                                                   tgGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   <  2:604583/130‑1 (MQ=255)                                                           cTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCg                                                                  >  2:416634/1‑139 (MQ=255)                                                                     aTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   <  2:984444/112‑1 (MQ=255)                                                                     aTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   >  1:984444/1‑112 (MQ=255)                                                                     aTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCtggtgg                                                        >  2:464303/1‑139 (MQ=255)                                                                         ccTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCAtt                                                    <  1:1065583/139‑1 (MQ=255)                                                                              gATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCAtt                                                    >  2:1246945/1‑134 (MQ=255)                                                                              gATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCAtt                                                    <  1:1246945/134‑1 (MQ=255)                                                                                      tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGgcgc                                                              <  2:590025/116‑1 (MQ=255)                                                                                      tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGgcgc                                                              >  1:590025/1‑116 (MQ=255)                                                                                      tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCAtt                                                    >  2:1517803/1‑126 (MQ=255)                                                                                      tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCAtt                                                    <  1:1517803/126‑1 (MQ=255)                                                                                      tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGccacca                                       >  1:1254167/1‑139 (MQ=255)                                                                                        cGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTc                                                                                                      <  1:879522/74‑1 (MQ=255)                                                                                        cGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTc                                                                                                      >  2:879522/1‑74 (MQ=255)                                                                                        cGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCAcg                                     >  1:476357/1‑139 (MQ=255)                                                                                        cGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCAcg                                     >  2:1531597/1‑139 (MQ=255)                                                                                          gTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCAcgcg                                   >  1:435551/1‑139 (MQ=255)                                                                                          gTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTCATCTCATCCCGGCGCTGGTGGCATTTg                                                  <  2:1008453/124‑1 (MQ=255)                                                                                          gTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTGTATTTATCTCATCCCGGCGCTGGTGGCATTTg                                                  >  1:1008453/1‑124 (MQ=255)                                                                                           tGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACgcgc                                  <  1:1531597/139‑1 (MQ=255)                                                                                           tGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACgcgc                                  <  1:200539/139‑1 (MQ=255)                                                                                           tGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACgcgc                                  <  1:416634/139‑1 (MQ=255)                                                                                                tcAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGt                                                                                        <  2:170261/80‑1 (MQ=255)                                                                                                tcAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGt                                                                                        >  1:170261/1‑80 (MQ=255)                                                                                                         tcGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGcc                                                                                                             >  1:428214/1‑50 (MQ=255)                                                                                                         tcGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGcc                                                                                                             <  2:428214/50‑1 (MQ=255)                                                                                                         tcGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTAATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGcct                    >  2:998987/1‑137 (MQ=255)                                                                                                          cGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGtttat                                                                               >  1:432365/1‑79 (MQ=255)                                                                                                          cGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGtttat                                                                               <  2:432365/79‑1 (MQ=255)                                                                                                                 tGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTcc            >  1:456154/1‑139 (MQ=255)                                                                                                                   gCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCg                                                                                                            <  2:1597380/41‑1 (MQ=255)                                                                                                                   gCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCg                                                                                                            >  1:1597380/1‑41 (MQ=255)                                                                                                                   gCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCcgc          <  2:1254167/139‑1 (MQ=255)                                                                                                                       gCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGt                                                                                        >  2:1394087/1‑57 (MQ=255)                                                                                                                       gCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGt                                                                                        <  1:1394087/57‑1 (MQ=255)                                                                                                                           aTGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   <  2:115489/58‑1 (MQ=255)                                                                                                                           aTGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                   >  1:115489/1‑58 (MQ=255)                                                                                                                           aTGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCCGCGTAACaaa  >  2:1402361/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                  CCGCAGGGCTGGCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGATTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCCGCGTAACAAA  >  NC_000913/1081929‑1082189

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑