Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,641,619	T→C	intergenic (‑65/‑236)	cspB ← / → cspF	Qin prophage; cold shock‑like protein CspB/Qin prophage; cold shock protein CspF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,641,619	0	T	C	100.0%	204.9 / NA	55	intergenic (‑65/‑236)	cspB/cspF	Qin prophage; cold shock‑like protein CspB/Qin prophage; cold shock protein CspF
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (22/33);  total (22/33)

AACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTTAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGT  >  NC_000913/1641483‑1641753                                                                                                                                         |                                                                                                                                       aaCAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAAt                                                                                                                                     >  2:198740/1‑140 (MQ=255) aaCAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAAt                                                                                                                                     >  1:246485/1‑140 (MQ=255)     ggAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGga                                                                                                                                 <  1:318073/140‑1 (MQ=255)      gagaAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGgag                                                                                                                                >  2:136216/1‑140 (MQ=255)       agaAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGgaga                                                                                                                               <  2:522961/140‑1 (MQ=255)       agaAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGgaga                                                                                                                               <  2:205578/140‑1 (MQ=255)                gCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAaag                                                                                                                      <  2:23946/140‑1 (MQ=255)                 ccGAAATCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAaaga                                                                                                                     <  1:447216/140‑1 (MQ=255)                 ccGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAaaga                                                                                                                     <  1:198740/140‑1 (MQ=255)                               aGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAAt                                                                                                       <  1:80668/140‑1 (MQ=255)                                 cGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATaa                                                                                                     >  2:309849/1‑140 (MQ=255)                                 cGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATaa                                                                                                     >  2:374180/1‑140 (MQ=255)                                   ttAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAaca                                                                                                   >  2:451596/1‑140 (MQ=255)                                           ttttACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAAt                                                                                           >  2:418342/1‑140 (MQ=255)                                           ttttACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAAt                                                                                           >  2:247188/1‑140 (MQ=255)                                              tACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATgag                                                                                        <  1:287178/140‑1 (MQ=255)                                               aCTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATgaga                                                                                       <  1:451596/140‑1 (MQ=255)                                                cTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGaa                                                                                      <  1:44227/140‑1 (MQ=255)                                                   aaCCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAacac                                                                                                  <  1:353539/125‑1 (MQ=255)                                                   aaCCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAacac                                                                                                  >  2:353539/1‑125 (MQ=255)                                                   aaCCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTg                                                                                   >  1:502471/1‑140 (MQ=255)                                                      cAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCtt                                                                                <  1:374180/140‑1 (MQ=255)                                                        gTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTa                                                                              <  2:526972/140‑1 (MQ=255)                                                              ttATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAac                                                                        <  1:247188/140‑1 (MQ=255)                                                              ttATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAac                                                                        <  1:451907/140‑1 (MQ=255)                                                               tATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAact                                                                       <  1:101661/140‑1 (MQ=255)                                                                   tGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACtt                                                                   <  2:246485/140‑1 (MQ=255)                                                                   tGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACtt                                                                   <  1:309388/140‑1 (MQ=255)                                                                       aTTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGta                                                               >  2:161602/1‑140 (MQ=255)                                                                                  cTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGtt                                                    >  1:113218/1‑140 (MQ=255)                                                                                    tAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGttct                                                  >  2:506744/1‑140 (MQ=255)                                                                                          gAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAAc                                            >  1:53060/1‑140 (MQ=255)                                                                                          gAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAAc                                            >  2:294945/1‑140 (MQ=255)                                                                                           aGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAAcc                                           >  1:233030/1‑140 (MQ=255)                                                                                            gCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCg                                          >  1:140396/1‑140 (MQ=255)                                                                                             ccTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGa                                         <  2:233030/140‑1 (MQ=255)                                                                                                 tCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCa                                     <  1:506744/140‑1 (MQ=255)                                                                                                   ggCATAAATGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAAt                                   <  2:140396/140‑1 (MQ=255)                                                                                                          aTGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCAt                                >  2:241831/1‑136 (MQ=255)                                                                                                          aTGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCAt                                <  1:241831/136‑1 (MQ=255)                                                                                                          aTGGTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAAc                            >  1:353544/1‑140 (MQ=255)                                                                                                             gTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACGCCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCa                         <  1:136216/140‑1 (MQ=255)                                                                                                             gTTTGCATAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCa                         <  1:440998/140‑1 (MQ=255)                                                                                                                   aTAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTg                   <  1:97521/140‑1 (MQ=255)                                                                                                                   aTAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTg                   <  1:282262/140‑1 (MQ=255)                                                                                                                   aTAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTg                   <  1:309849/140‑1 (MQ=255)                                                                                                                    tAACAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGa                  <  2:353544/140‑1 (MQ=255)                                                                                                                       cAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGtt                    >  2:425466/1‑135 (MQ=255)                                                                                                                       cAGAAACGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGtt                    <  1:425466/135‑1 (MQ=255)                                                                                                                            aCGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATg           <  2:322180/139‑1 (MQ=255)                                                                                                                            aCGACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATg           >  1:322180/1‑139 (MQ=255)                                                                                                                              gACTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAg        <  1:294945/140‑1 (MQ=255)                                                                                                                                cTTCGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCa      <  1:418342/140‑1 (MQ=255)                                                                                                                                   cGTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATg   >  2:81017/1‑140 (MQ=255)                                                                                                                                    gTACTCAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGt  <  1:161602/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                       AACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACATTCTACATTCCTTAACTTGAGCCTTTCGGCATAAATGGTTTGCATAACAGAAACGACTTCGTACTTAATTGGAGAGACTCAAAGAAGGAATAAGTGAATAACACCTGAAATGAGAACTGCTTTAGTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGT  >  NC_000913/1641483‑1641753

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: ‑