Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,203,224	G→A	*67* (TAG→TAA)	croE →	e14 prophage, putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,203,224	0	G	A	100.0%	167.2 / NA	52	*67* (TAG→TAA)	croE	e14 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/26);  total (26/26)

TGGTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAGCAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAG  >  NC_000913/1203109‑1203350                                                                                                                    |                                                                                                                               tGGTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAAcc                                                                                                         <  2:328470/139‑1 (MQ=255)   gTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTc                                                                                                                    <  2:1447878/126‑1 (MQ=255)   gTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTc                                                                                                                    >  1:1447878/1‑126 (MQ=255)   gTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACca                                                                                                        >  1:729730/1‑138 (MQ=255)   gTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACca                                                                                                        <  2:729730/138‑1 (MQ=255)         aaTGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACg                                                                                                 >  2:1342425/1‑139 (MQ=255)           tGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGAt                                                                                               >  1:1171184/1‑139 (MQ=255)           tGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGAt                                                                                               <  1:304724/139‑1 (MQ=255)              cTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAg                                                                                                     <  2:1552938/130‑1 (MQ=255)              cTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAg                                                                                                     >  1:1552938/1‑130 (MQ=255)                         ccAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTgg                                                                                 >  2:1343978/1‑139 (MQ=255)                           aGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGt                                                                               <  1:1342425/139‑1 (MQ=255)                            gTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTa                                                                              <  1:806127/139‑1 (MQ=255)                               ttGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGc                                                                           <  2:1171184/139‑1 (MQ=255)                                                 ttGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTa                                                                              <  1:1441442/118‑1 (MQ=255)                                                 ttGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTa                                                                              >  2:1441442/1‑118 (MQ=255)                                                 ttGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGaa                                                                 >  2:1329960/1‑131 (MQ=255)                                                 ttGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGaa                                                                 <  1:1329960/131‑1 (MQ=255)                                                        aTACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGcc                                                  >  1:1399590/1‑139 (MQ=255)                                                            acaTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAg                                              <  1:1343978/139‑1 (MQ=255)                                                              aTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTg                                                                    <  1:90949/115‑1 (MQ=255)                                                              aTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTg                                                                    >  2:90949/1‑115 (MQ=255)                                                              aTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTg                                            >  1:1147989/1‑139 (MQ=255)                                                               tCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTgg                                           <  2:1399590/139‑1 (MQ=255)                                                               ataagagacagtACGAAATCTGACTTGAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATGTTTAACCACAGAACGATGAATCTAATCGTAGGTAAGCATCACGTGAAAATAGAAAAACAGCCTGAGTgg                                           <  1:1062943/128‑1 (MQ=255)                                                                   gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAAttttt                                                                                                             <  2:736196/69‑1 (MQ=255)                                                                   gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAAttttt                                                                                                             >  1:736196/1‑69 (MQ=255)                                                                   gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTgg                                           >  2:389591/1‑135 (MQ=255)                                                                   gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTgg                                           <  1:389591/135‑1 (MQ=255)                                                                       aaTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGaa                                   <  1:952482/139‑1 (MQ=255)                                                                        aTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAAc                                                                                                          >  2:26519/1‑67 (MQ=255)                                                                        aTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAAc                                                                                                          <  1:26519/67‑1 (MQ=255)                                                                                   tGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTgg                                                                                 <  1:1215518/81‑1 (MQ=255)                                                                                   tGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTgg                                                                                 >  2:1215518/1‑81 (MQ=255)                                                                                     aCTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCt                               <  1:44008/129‑1 (MQ=255)                                                                                     aCTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCt                               >  2:44008/1‑129 (MQ=255)                                                                                     aCTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGaaaaa                     >  1:1484235/1‑139 (MQ=255)                                                                                     aCTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGACTGAGTGGTACGTGAAAGCTGTCAGaaaaa                     >  1:480981/1‑139 (MQ=255)                                                                                     aCTTAAGACCGGATATCTATCCGAAAGACTAACAGAACACTTTCAATATTTAACCACAAAACGATGACGCTAATCGTGGGTAAGCATGACTGGAAAATAGAAAAACAGCCTGAGTGGTACGCGAAAGcctgtctcttat                     >  2:1062943/1‑128 (MQ=255)                                                                                               ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACca                                                                                                        <  1:20523/46‑1 (MQ=255)                                                                                               ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACca                                                                                                        >  2:20523/1‑46 (MQ=255)                                                                                               ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAg                                                                                                     <  2:1115383/49‑1 (MQ=255)                                                                                               ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAg                                                                                                     >  1:1115383/1‑49 (MQ=255)                                                                                                gATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCt                                                 <  1:431042/100‑1 (MQ=255)                                                                                                gATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCt                                                 >  2:431042/1‑100 (MQ=255)                                                                                                     ctatcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAg                                              >  2:1031753/1‑98 (MQ=255)                                                                                                     ctatcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAg                                              <  1:1031753/98‑1 (MQ=255)                                                                                                        tcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATc                                                                                     >  2:681840/1‑56 (MQ=255)                                                                                                        tcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATc                                                                                     <  1:681840/56‑1 (MQ=255)                                                                                                        tcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAg  >  2:1650052/1‑139 (MQ=255)                                                                                                            caaGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAg                                                                            >  1:1043065/2‑61 (MQ=255)                                                                                                            aaaGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAg                                                                            <  2:1043065/61‑1 (MQ=255)                                                                                                                    |                                                                                                                               TGGTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAGCAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAG  >  NC_000913/1203109‑1203350

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: ‑