Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,363,696	T→C	F16S (TTC→TCC)	pspD →	phage shock protein PspD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,363,696	0	T	C	100.0%	228.5 / NA	60	F16S (TTC→TCC)	pspD	phage shock protein PspD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/33);  total (27/33)

TACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTTGCT  >  NZ_CP009273/1363616‑1363781                                                                                 |                                                                                      tACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGc                                                                              >  1:1240345/1‑90 (MQ=255) tACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGc                                                                              >  1:2227455/1‑90 (MQ=255)     tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                          <  1:866385/90‑1 (MQ=255)     tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                          <  1:1558657/90‑1 (MQ=255)     tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                          <  2:840142/90‑1 (MQ=255)     tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                          <  1:2369358/90‑1 (MQ=255)     tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                          <  1:2862713/90‑1 (MQ=255)     tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                          <  2:2667814/90‑1 (MQ=255)       gCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCaa                                                                        >  2:54868/1‑90 (MQ=255)        ccGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAg                                                                       <  2:532339/90‑1 (MQ=255)        ccGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAg                                                                       <  1:215617/90‑1 (MQ=255)          gTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCt                                                                     >  1:1406614/1‑90 (MQ=255)          gTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCt                                                                     >  2:439594/1‑90 (MQ=255)           tttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTg                                                                    >  1:599128/1‑90 (MQ=255)            ttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                          <  2:307624/83‑1 (MQ=255)            ttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                          >  1:307624/1‑83 (MQ=255)            ttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTgg                                                                   <  1:529173/90‑1 (MQ=255)               cGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc                                                                <  2:2326000/90‑1 (MQ=255)                 tCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActt                                                              <  1:2063384/90‑1 (MQ=255)                 tCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActt                                                              <  2:3009153/90‑1 (MQ=255)                           ggAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                    <  2:1009390/90‑1 (MQ=255)                           ggAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                    <  2:245636/90‑1 (MQ=255)                           ggAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                    <  2:599128/90‑1 (MQ=255)                              aaGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTgc                                                 >  1:225281/1‑90 (MQ=255)                                  tATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTa                                             <  2:2227455/90‑1 (MQ=255)                                  tATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTa                                             <  2:2029503/90‑1 (MQ=255)                                   aTGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTAt                                            >  2:686828/1‑90 (MQ=255)                                     gAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATgg                                          >  2:2801862/1‑90 (MQ=255)                                          cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg                                     >  2:220335/1‑90 (MQ=255)                                          cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg                                     >  2:510243/1‑90 (MQ=255)                                          cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg                                     >  2:757581/1‑90 (MQ=255)                                          cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg                                     >  1:1137800/1‑90 (MQ=255)                                          cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg                                     >  1:1894742/1‑90 (MQ=255)                                          cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg                                     >  1:204289/1‑90 (MQ=255)                                           tCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcggc                                    <  1:54868/90‑1 (MQ=255)                                            cGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGt                                                                  <  2:2504184/59‑1 (MQ=255)                                            cGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGt                                                                  >  1:2504184/1‑59 (MQ=255)                                              cTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCggg                                 >  1:1943282/1‑90 (MQ=255)                                              cTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCggg                                 <  1:757581/90‑1 (MQ=255)                                                 gCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActt                                                              <  1:1606587/58‑1 (MQ=255)                                                 gCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActt                                                              >  2:1606587/1‑58 (MQ=255)                                                   aaCAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTgg                            <  2:1240345/90‑1 (MQ=255)                                                      aGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActtctt                                                           <  2:1516985/56‑1 (MQ=255)                                                      aGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActtctt                                                           >  1:1516985/1‑56 (MQ=255)                                                      aGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGGGTGgggg                         >  1:1875143/1‑90 (MQ=255)                                                       ggCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGGGTGGCggg                        >  1:222579/1‑90 (MQ=255)                                                       ggCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGGGTGGCggg                        >  1:2091244/1‑90 (MQ=255)                                                       ggCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGGGTGGCggg                        >  1:108396/1‑90 (MQ=255)                                                        gCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCgggg                       >  2:1854163/1‑89 (MQ=255)                                                            ggCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTggg                   <  2:170974/90‑1 (MQ=255)                                                              cAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTGCTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCg                 <  1:1824864/90‑1 (MQ=255)                                                              cAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTgggag                 <  1:1162138/90‑3 (MQ=255)                                                                 aaGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATa              <  2:2524576/90‑1 (MQ=255)                                                                    gTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATaaaa           <  1:2831690/90‑1 (MQ=255)                                                                      aaaGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                    <  1:2708843/47‑1 (MQ=255)                                                                      aaaGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                    >  2:2708843/1‑47 (MQ=255)                                                                          ccTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGtt     <  2:1894742/90‑1 (MQ=255)                                                                             ggTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                    >  2:914042/1‑40 (MQ=255)                                                                             ggTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                    <  1:914042/40‑1 (MQ=255)                                                                             ggTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTTGCt  <  2:2190796/90‑1 (MQ=255)                                                                                 |                                                                                      TACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTTGCT  >  NZ_CP009273/1363616‑1363781

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑