Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	136,457	(T)8→7	coding (8/867 nt)	speE ←	spermidine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	136,450	0	T	.	95.7%	173.7 / 2.5	46	coding (15/867 nt)	speE	spermidine synthase
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base . (22/22);  total (23/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

CGCCATCCAGCGCCATTACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTGTTTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAGGGATTATTTGACGTAGGCA  >  NC_000913/136311‑136585                                                                                                                                            |                                                                                                                                        cGCCATCCAGCGCCATTACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTGt                                                                                                                                         >  1:501988/1‑140 (MQ=255) cGCCATCCAGCGCCATTACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGAACTCCCCAAACTGGCCGTGGAGCGTTTTATGACCCTGt                                                                                                                                         >  1:727545/1‑140 (MQ=255)      tCCAGCGCCATTACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTGtttttt                                                                                                                                    >  2:157032/1‑140 (MQ=255)      tCCAGCGCCATTACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTGtttttt                                                                                                                                    >  2:444111/1‑140 (MQ=255)       ccAGCGCCATTACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTGttttttt                                                                                                                                   <  1:157032/140‑1 (MQ=255)             ccATTACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCa                                                                                                                            >  2:153992/1‑140 (MQ=255)              cATTACGCGACCAAATGAAGCGTTCTCAAAAGTGATCAGATCCTGGTGGTCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCAt                                                                                                                           <  2:264908/140‑1 (MQ=255)                ttACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATgg                                                                                                                         >  1:557913/1‑140 (MQ=255)                 tACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATggg                                                                                                                        <  1:128242/140‑1 (MQ=255)                             tGCAGCGTTCTCAAAAATGATCAGATTCTGGTGATAGGTCTTTTGATGATACAGAACGTTTTCTACCACAAAGTACTGCCCAAACTGGTCGTGTAGGGTTTCATGCCAC‑GGTTTTTTTCGGCCATGGGTTGATAcctcct                                                                                                            <  2:727545/140‑1 (MQ=255)                                    ttCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTaa                                                                                                     <  2:124008/140‑1 (MQ=255)                                      ctcAAAAATGATCAGCTCCTGGAGACCGGCCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAaca                                                                                                   <  1:203787/140‑1 (MQ=255)                                      ctcAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAaca                                                                                                   >  2:145011/1‑140 (MQ=255)                                                      tCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGgc                                                                                   >  2:27881/1‑140 (MQ=255)                                                       ccTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGgcg                                                                                  <  1:444111/140‑1 (MQ=255)                                                        cTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGgcgc                                                                                 <  1:27881/140‑1 (MQ=255)                                                              aTCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAATGGCGCAACata                                                                           <  1:725612/140‑1 (MQ=255)                                                                     ttttCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAggg                                                                                    >  2:167775/1‑124 (MQ=255)                                                                     ttttCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAggg                                                                                    <  1:167775/124‑1 (MQ=255)                                                                             aTACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTgtc                                                            >  1:716612/1‑138 (MQ=255)                                                                             aTACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGAc                                                            >  2:398991/1‑140 (MQ=255)                                                                             aTACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGAc                                                            <  1:145011/140‑1 (MQ=255)                                                                                  gAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCgg                                                       <  1:693183/140‑1 (MQ=255)                                                                                       ttATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCa                                                  <  2:106730/140‑1 (MQ=255)                                                                                       ttATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCa                                                  <  1:398991/140‑1 (MQ=255)                                                                                       ttATCTACCGCAAAGGACTGCCCAATCTGTTCGTGTAACGTTTCTTGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCa                                                  <  1:277591/140‑1 (MQ=255)                                                                                        tATCTACCGCAAAGTGCTGCCCTAAATGGCCGTGTAGAGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCAc                                                 <  1:222427/140‑1 (MQ=255)                                                                                        tATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACcg                                                          <  2:32578/131‑1 (MQ=255)                                                                                        tATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACcg                                                          >  1:32578/1‑131 (MQ=255)                                                                                            tACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTCAAAAAAGGTCGCGACATAATAGCTATCATTGACCGCGGATGCACGGTc                                             >  2:222427/1‑140 (MQ=255)                                                                                               cGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAat                                          >  1:63937/1‑140 (MQ=255)                                                                                               cGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAat                                          >  2:463811/1‑140 (MQ=255)                                                                                                gCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCTTGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAATAAGGGCGCAACAAAATCGCTAACATAGACCGCGGATGCACGGTCAata                                         >  2:277591/1‑140 (MQ=255)                                                                                                gCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAata                                         >  2:563809/1‑140 (MQ=255)                                                                                                 cAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCAAACATTGACCGCGTATGCACGGTCAatat                                        >  1:330766/1‑140 (MQ=255)                                                                                                         tGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTc                                             >  2:544608/1‑127 (MQ=255)                                                                                                         tGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTc                                             <  1:544608/127‑1 (MQ=255)                                                                                                           cccAAACTGGTCGTGTAGCGTTTCATGCCACTGTTTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTAc                                  <  2:663158/137‑1 (MQ=255)                                                                                                           cccAAACTGGTCGTGTAGCGTTTCATGCCACTGTTTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTAc                                  >  1:663158/1‑137 (MQ=255)                                                                                                           cccAAACTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACaaaa                              <  1:165661/140‑1 (MQ=255)                                                                                                           acagaaCTGGTCGTGTCGCGTTTCATGCCACCG‑ATCTTTGCGGCCATGTGTTGATCCCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACaaaa                              <  2:330705/136‑1 (MQ=255)                                                                                                                aCTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAggaa                         >  1:633194/1‑138 (MQ=255)                                                                                                                aCTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTa                         >  1:417017/1‑140 (MQ=255)                                                                                                                 cTGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTAt                        <  1:153992/140‑1 (MQ=255)                                                                                                                  tGGTCGTGTAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATc                       <  2:501988/140‑1 (MQ=255)                                                                                                                          tAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAGGGatta               >  1:133946/1‑140 (MQ=255)                                                                                                                          tAGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATAGTTCTACAAACAGGAATCAgggctgt               >  1:330705/1‑136 (MQ=255)                                                                                                                           aGCGTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGTCCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAGGGattat              <  2:716612/140‑1 (MQ=255)                                                                                                                              gTTTCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAGGGATTATTTg           >  1:179692/1‑140 (MQ=255)                                                                                                                               tttCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAgg                    <  2:379596/130‑1 (MQ=255)                                                                                                                               tttCATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAgg                    >  1:379596/1‑130 (MQ=255)                                                                                                                                  cATGCCACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAGGGATTATTTGACGt       <  1:463811/140‑1 (MQ=255)                                                                                                                                       cACTG‑TTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAGGGATTATTTGACGTAGGCa  >  1:620770/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                        CGCCATCCAGCGCCATTACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGTTATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTGTTTTTTTTCGGCCATGGGTTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCACGGTCAATATTTCTACAAAAAGGTATCAGGGATTATTTGACGTAGGCA  >  NC_000913/136311‑136585

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑