Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,228,728	C→T	pseudogene (31/150 nt)	mdtQ ←	pseudogene, putative channel/filament proteins

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,228,728	0	C	T	100.0%	175.8 / NA	51	pseudogene (31/150 nt)	mdtQ	pseudogene, putative channel/filament proteins
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/29);  total (22/29)

CATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGCGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGCAATAAAACGAC  >  NC_000913/2228606‑2228857                                                                                                                           |                                                                                                                                  cATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAg                                                                                                                   >  2:28036/1‑139 (MQ=255)          cgacGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACTCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGa                                                                                                          >  1:682423/4‑139 (MQ=255)                gggTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATg                                                                                                    <  1:784037/139‑1 (MQ=255)                    aaTGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATggggg                                                                                                >  1:807843/1‑139 (MQ=255)                         ggTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACA‑CCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGaataat                                                                                          >  2:528143/1‑139 (MQ=255)                                     tgCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGaaa                                                                               >  2:523541/1‑139 (MQ=255)                                          cGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       <  2:330404/126‑1 (MQ=255)                                          cGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       >  1:330404/1‑126 (MQ=255)                                            ggCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTgcg                                                                        <  1:523541/139‑1 (MQ=255)                                             gCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTgcgc                                                                       <  1:295729/139‑1 (MQ=255)                                             gCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTgcgc                                                                       <  1:404997/139‑1 (MQ=255)                                              cGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGcgcg                                                                      <  1:340814/139‑1 (MQ=255)                                               gTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATg                                                                                                    <  2:80451/108‑1 (MQ=255)                                               gTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATg                                                                                                    >  1:80451/1‑108 (MQ=255)                                               gTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCgg                                                                     >  1:403912/1‑139 (MQ=255)                                                tttGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGga                                                                    <  2:696248/139‑1 (MQ=255)                                                      ggCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTAc                                                              >  1:1152456/1‑139 (MQ=255)                                                         ttAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCgt                                                           <  1:499338/139‑1 (MQ=255)                                                         ttAACGCCTGGC‑GGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCgtg                                                          >  2:176531/1‑139 (MQ=255)                                                                cTGGC‑GGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCg                                                   <  1:176531/139‑1 (MQ=255)                                                                 tGGCGGGTTTCATGCATAGGCCCACGCCCGGCCAGCATCAGTAACAGCGGCAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTAGCg                                                   >  1:148528/1‑139 (MQ=255)                                                                    cGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGata                                                <  2:403912/139‑1 (MQ=255)                                                                      ggTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGatata                                              <  1:403737/139‑1 (MQ=255)                                                                       gTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGatatat                                             >  1:719343/1‑139 (MQ=255)                                                                             tGCATAGGCGCACA‑CCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAg                                      <  1:528143/139‑1 (MQ=255)                                                                                   ggCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTcg                                 <  2:682423/139‑1 (MQ=255)                                                                                    gcgcACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       >  2:671221/1‑84 (MQ=255)                                                                                    gcgcACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       <  1:671221/84‑1 (MQ=255)                                                                                     cgcACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTcgcg                               <  2:376353/139‑1 (MQ=255)                                                                                     cgcACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTcgcg                               <  1:252839/139‑1 (MQ=255)                                                                                      gcACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGt                              <  2:1152456/139‑1 (MQ=255)                                                                                       cacaCCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTAcc                                                             >  2:375459/1‑107 (MQ=255)                                                                                       cacaCCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTAcc                                                             <  1:375459/107‑1 (MQ=255)                                                                                        acacCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTgg                            <  1:883907/139‑1 (MQ=255)                                                                                         cacCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAg                                                                             >  2:926787/1‑89 (MQ=255)                                                                                         cacCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAg                                                                             <  1:926787/89‑1 (MQ=255)                                                                                            ccGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATgg                                                                                                   >  1:91646/1‑64 (MQ=255)                                                                                            ccGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATgg                                                                                                   <  2:91646/64‑1 (MQ=255)                                                                                                    cATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       >  1:1156849/1‑68 (MQ=255)                                                                                                    cATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       <  2:1156849/68‑1 (MQ=255)                                                                                                       cAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGc             <  2:463291/139‑1 (MQ=255)                                                                                                       cAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGc             <  2:807843/139‑1 (MQ=255)                                                                                                          tAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTcgcg                               >  1:175343/1‑118 (MQ=255)                                                                                                          tAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTcgcg                               <  2:175343/118‑1 (MQ=255)                                                                                                              aGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGt                              >  2:282884/1‑115 (MQ=255)                                                                                                              aGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGt                              <  1:282884/115‑1 (MQ=255)                                                                                                                cGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       <  2:441106/56‑1 (MQ=255)                                                                                                                cGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       >  1:441106/1‑56 (MQ=255)                                                                                                                  gAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTgcgc                                                                       >  2:1111851/1‑70 (MQ=255)                                                                                                                  gAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTgcgc                                                                       <  1:1111851/70‑1 (MQ=255)                                                                                                                  gAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGCAATAAAACGAc  >  2:452610/1‑139 (MQ=255)                                                                                                                           |                                                                                                                                  CATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGCGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGCAATAAAACGAC  >  NC_000913/2228606‑2228857

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑