Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,366,935	C→T	*326* (TAG→TAA)	pspF ←	psp operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,366,935	0	C	T	100.0%	217.8 / NA	68	*326* (TAG→TAA)	pspF	psp operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (38/30);  total (38/30)

GCTGAGCGATTAATAGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGCTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTGCAGCAACTCTTTTTCCTGCT  >  NC_000913/1366803‑1367059                                                                                                                                     |                                                                                                                              gcTGAGCGATTAATAGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATc                                                                                                                         >  1:610204/1‑139 (MQ=255)                 cccAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGTATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTcaaca                                                                                                        >  1:412594/1‑139 (MQ=255)                    aaCGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAAcg                                                                                                     >  1:1057611/1‑139 (MQ=255)                      cGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAAcgcg                                                                                                   >  1:844066/1‑139 (MQ=255)                      cGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATATATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAAcgcg                                                                                                   >  1:1066208/1‑139 (MQ=255)                         aataatGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCgg                                                                                                <  2:210976/139‑1 (MQ=255)                           taatGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGaa                                                                                              <  2:844066/139‑1 (MQ=255)                                     tgcgctgcgcTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATaa                                                                                    >  1:569576/1‑139 (MQ=255)                                       cgctgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGt                                                                                                                     >  1:1207606/1‑105 (MQ=255)                                       cgctgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGt                                                                                                                     <  2:1207606/105‑1 (MQ=255)                                         ctgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAAcgcgcg                                                                                                 >  1:18530/1‑122 (MQ=255)                                         ctgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAAcgcgcg                                                                                                 <  2:18530/122‑1 (MQ=255)                                          tgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGt                                                                                                                     <  1:988591/102‑1 (MQ=255)                                          tgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGaa                                                                                              >  2:430305/1‑124 (MQ=255)                                          tgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGaa                                                                                              <  1:430305/124‑1 (MQ=255)                                          tgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTaa                                                                               >  2:825000/1‑139 (MQ=255)                                          tgcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGACGAATAAAGCATTCACGCCGCATCCGGCAAGATGTATTGCTCAACTTCGTTAAATCTGGt                                                                                                                     >  2:988591/1‑102 (MQ=255)                                           gcgctTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAAc                                                                              <  2:1057611/139‑1 (MQ=255)                                                      gCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTc                                                                   >  2:1127317/1‑139 (MQ=255)                                                           cAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCcg                                                              >  2:1264841/1‑139 (MQ=255)                                                           cAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCcg                                                              >  1:112918/1‑139 (MQ=255)                                                                gacgTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCgcgcgc                                                         >  1:12134/1‑139 (MQ=255)                                                                    tATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAAcgcg                                                                                                   <  2:1539915/93‑1 (MQ=255)                                                                    tATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAAcgcg                                                                                                   >  1:1539915/1‑93 (MQ=255)                                                                       tGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGt                                                  <  2:192707/139‑1 (MQ=255)                                                                       tGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGt                                                  <  1:825000/139‑1 (MQ=255)                                                                        gATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGCTTTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGt                                                  <  2:610204/139‑1 (MQ=255)                                                                             tgtatgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACtg                                                                                           <  2:716735/92‑1 (MQ=255)                                                                             tgtatgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACtg                                                                                           >  1:716735/1‑92 (MQ=255)                                                                               tatgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTc                                          >  2:317735/1‑139 (MQ=255)                                                                                atgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACtgatg                                                                                        <  2:1584201/92‑1 (MQ=255)                                                                                atgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACtgatg                                                                                        >  1:1584201/1‑92 (MQ=255)                                                                                atgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAg                                                                                   >  2:276358/1‑97 (MQ=255)                                                                                atgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTGAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAg                                                                                   <  1:276358/97‑1 (MQ=255)                                                                                 tgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTccc                                        <  2:1066208/139‑1 (MQ=255)                                                                                 tgCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTccc                                        >  1:1230003/1‑139 (MQ=255)                                                                                  gCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCcgcg                                                            >  2:526670/1‑118 (MQ=255)                                                                                  gCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCcgca                                                            <  1:526670/118‑2 (MQ=255)                                                                                   ccGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGTACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCtt                                      >  2:1527314/1‑139 (MQ=255)                                                                                   ccGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCtt                                      >  1:619051/1‑139 (MQ=255)                                                                                     gAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCttgt                                    <  1:317735/139‑1 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGaa                                                                                              <  1:750695/70‑1 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGaa                                                                                              >  2:750695/1‑70 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAAcccc                                                                           >  2:1453683/1‑89 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAAcccc                                                                           <  1:1453683/89‑1 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCt                                                        <  2:313632/108‑1 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCt                                                        >  1:313632/1‑108 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTccc                                        >  1:1272639/1‑124 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTccc                                        <  2:1272639/124‑1 (MQ=255)                                                                                                tCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAg                         >  2:1134828/1‑139 (MQ=255)                                                                                                      cgcATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTgcag                   <  2:112918/139‑1 (MQ=255)                                                                                                       gcATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACtgatga                                                                                       <  1:1513000/70‑1 (MQ=255)                                                                                                       gcATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACtgatga                                                                                       >  2:1513000/1‑70 (MQ=255)                                                                                                       gcATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTgcagc                  <  1:1264841/139‑1 (MQ=255)                                                                                                       gcATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTgcagc                  >  2:1074758/1‑139 (MQ=255)                                                                                                        cATCCGGCAAGTTGTATTGCTCAAGTTCGTTAAATCTGGTGC‑TTTTTCAACAAcgcg                                                                                                   >  1:1091827/1‑57 (MQ=255)                                                                                                        cATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAAcgcg                                                                                                   <  2:1091827/57‑1 (MQ=255)                                                                                                        cATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAAc                                                                                             <  1:665496/63‑1 (MQ=255)                                                                                                        cATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAAc                                                                                             >  2:665496/1‑63 (MQ=255)                                                                                                        cATCCGGCAAGTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTgcagca                 >  1:154933/1‑139 (MQ=255)                                                                                                                  gTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGaa                                                                                              <  1:701982/52‑1 (MQ=255)                                                                                                                  gTTGTATTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGaa                                                                                              >  2:701982/1‑52 (MQ=255)                                                                                                                       aTTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTGCAGCAACTCTTTTTCctgct  <  2:154933/139‑1 (MQ=255)                                                                                                                       aTTGCTCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTGCAGCAACTCTTTTTCctgct  >  1:442690/1‑139 (MQ=255)                                                                                                                            tCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACtgatga                                                                                       >  2:1185839/1‑49 (MQ=255)                                                                                                                            tCAACTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACtgatga                                                                                       <  1:1185839/49‑1 (MQ=255)                                                                                                                                cTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTgcagca                 >  1:1311543/1‑115 (MQ=255)                                                                                                                                cTTCGTTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTgcagca                 <  2:1311543/115‑1 (MQ=255)                                                                                                                                     |                                                                                                                              GCTGAGCGATTAATAGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCAAGTTGTATTGCTCAACTTCGCTAAATCTGGTGC‑TTTTTCAACAACGCGCGGAACTGATGATAAGTTAACCCCAGTAATTCAGCCGCGCGCTTCTGGTTATATTTCCCTTGTTGCAAACTGAGTTGCAGCAACTCTTTTTCCTGCT  >  NC_000913/1366803‑1367059

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑