Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,883,865	G→A	intergenic (‑136/‑161)	dnaA ← / → ysdD	chromosomal replication initiator protein DnaA/protein YsdD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,883,865	0	G	A	100.0%	131.8 / NA	38	intergenic (‑136/‑161)	dnaA/ysdD	chromosomal replication initiator protein DnaA/protein YsdD
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (16/22);  total (16/22)

GGCGGACTCCACTCGAACAAAAGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCCGCGAGGCGGGCACGA  >  NC_000913/3883730‑3884000                                                                                                                                        |                                                                                                                                        ggcggACTCCACTCGAACAAAAGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACACACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACaaa                                                                                                                                     <  1:103983/140‑1 (MQ=255)    ggACTCCACTCGAACAAAAGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACg                                                                                                                                  <  2:416556/140‑1 (MQ=255)      aCTCCACTCGAACAAAAGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGAt                                                                                                                                <  2:101457/140‑1 (MQ=255)               gAACAAAAGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACcgc                                                                                                                       <  2:569384/140‑1 (MQ=255)                    aaaGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATc                                                                                                                  <  1:741953/140‑1 (MQ=255)                    aaaGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATc                                                                                                                  <  2:295559/140‑1 (MQ=255)                    aaaGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATc                                                                                                                  <  2:146647/140‑1 (MQ=255)                    aaaGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATc                                                                                                                  <  2:75496/140‑1 (MQ=255)                    aaaGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATc                                                                                                                  <  1:434407/140‑1 (MQ=255)                                       gCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAag                                                                                               <  2:640650/140‑1 (MQ=255)                                          gAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAgaga                                                                                            >  1:500727/1‑140 (MQ=255)                                           aaaCATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGAt                                                                                           >  1:602579/1‑140 (MQ=255)                                                ttCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGAtcttct                                                                                      >  2:403618/1‑140 (MQ=255)                                                        tgttgACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTca                                                                              <  2:11617/140‑1 (MQ=255)                                                          ttgtcgtacgtCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTcaca                                                                            >  1:779514/5‑140 (MQ=255)                                                             acgtacgtCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGAt                                                                         >  1:143728/1‑140 (MQ=255)                                                                tacgtCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGAtttt                                                                      <  1:360969/140‑1 (MQ=255)                                                                 acgtCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTc                                                                     <  2:602579/140‑1 (MQ=255)                                                                  cgtCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTcc                                                                    >  2:128758/1‑140 (MQ=255)                                                                                tGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAg                                                      >  1:756143/1‑140 (MQ=255)                                                                                  cTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGa                                                    <  2:729328/140‑1 (MQ=255)                                                                                            aCGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGaa                                          >  1:520810/1‑140 (MQ=255)                                                                                            aCGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGaa                                          >  1:149812/1‑140 (MQ=255)                                                                                                aCGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCg                                      <  1:784248/140‑1 (MQ=255)                                                                                                aCGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCg                                      <  2:756143/140‑1 (MQ=255)                                                                                                  gAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCt                                    <  2:784504/140‑1 (MQ=255)                                                                                                   aaCCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTa                                   <  2:629457/140‑1 (MQ=255)                                                                                                    aCCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTaa                                  <  2:580349/140‑1 (MQ=255)                                                                                                    aCCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTaa                                  <  2:181588/140‑1 (MQ=255)                                                                                                    aCCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTaa                                  >  1:426933/1‑140 (MQ=255)                                                                                                                       tGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCcgc               >  2:343297/1‑140 (MQ=255)                                                                                                                       tGCCCGATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCcgc               >  1:699616/1‑140 (MQ=255)                                                                                                                            gATCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCCGCGAGGc          >  2:245830/1‑140 (MQ=255)                                                                                                                              tCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCCGCGAGGCgg        >  2:561779/1‑140 (MQ=255)                                                                                                                              tCAAGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCCGCGAGGCgg        >  1:716860/1‑140 (MQ=255)                                                                                                                                aaGATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCCGCGAGGCGGGc      <  1:140459/140‑1 (MQ=255)                                                                                                                                  gATCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCCGCGAGGCGGGCAc    <  2:702054/140‑1 (MQ=255)                                                                                                                                    tCCTACAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCCGCGAGGCGGGCACGa  >  1:732871/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        GGCGGACTCCACTCGAACAAAAGTCGATAATGACTAAGGCTGAAACATTCATGATTGTTGACGTACGTCGAAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCCTGCCGCGAGGCGGGCACGA  >  NC_000913/3883730‑3884000

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑