Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	3,953,437	Δ1 bp	pseudogene (178/243 nt)	yifN ←	PemK toxin family pseudogene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,953,437	0	C	.	97.7%	193.1 / ‑1.9	44	pseudogene (178/243 nt)	yifN	PemK toxin family pseudogene
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base . (24/19);  minor base G (1/0);  total (25/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01

GTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACTCATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTCATTGATAACATTACTGGC  >  CP009273/3953301‑3953578                                                                                                                                         |                                                                                                                                              gTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCa                                                                                                                                       <  1:379474/144‑1 (MQ=255)  tCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACAtt                                                                                                                                 >  2:662399/1‑149 (MQ=255)      tCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCCTTGATTGATTTGATGCCCGCCCTCTGTATGTCTGCAACCAAAT‑ATGTGGCACACATTGAtt                                                                                                                             >  2:19127/1‑149 (MQ=255)        aaGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTg                                                                                                                                >  1:626241/1‑144 (MQ=255)        aaGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTaa                                                                                                                           <  2:742591/149‑1 (MQ=255)              agaAAACTTAGGGCCTTTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAg                                                                                                                          <  1:261690/144‑1 (MQ=255)               gaAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGa                                                                                                                         >  1:100593/1‑144 (MQ=255)               gaAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATAccc                                                                                                                    <  2:636796/149‑1 (MQ=255)                aaaaCTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTCTGAGCGATGTGGCATTGATTGACTTGATGACCGCCCTCTGGATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGGTACCct                                                                                                                   >  2:323510/1‑149 (MQ=255)                         ggCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGCTTAAGATACCCTCTGt                                                                                                               >  1:440421/1‑144 (MQ=255)                                   ggCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCACCTGTAAGTCCTTGc                                                                                                     >  1:60161/1‑144 (MQ=255)                                              cATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCAGTGATTGACTGGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGttt                                                                                     >  2:15514/1‑149 (MQ=255)                                                ttATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCATCT‑ATGTGGCAAACCTTGATTAAATAAGCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCg                                                                                   >  2:701649/1‑149 (MQ=255)                                                ttATCGGGGATGGTTATTTTATTGTCAATATATGAGCGATATGGCATTGATTGTCTTGATGACCGCCGTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCGTCTGTAAATCCTTGCTCTCTTTAATCTGTTTCg                                                                                   >  2:632200/1‑149 (MQ=255)                                                       ggATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCgac                                                                                 >  1:54686/1‑144 (MQ=255)                                                               attttattGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTAc                                                                    <  2:376569/149‑1 (MQ=255)                                                                 tttattGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTCCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCa                                                                  >  2:252475/1‑149 (MQ=255)                                                                  ttattGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTtgttgt                                                                      <  1:420663/144‑1 (MQ=255)                                                                       gTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGCTCTACCAg                                                                 <  1:768159/144‑1 (MQ=255)                                                                        tCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAgg                                                                >  1:155197/1‑144 (MQ=255)                                                                          aaTTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCtt                                                         >  2:220985/1‑149 (MQ=255)                                                                          aaTTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ACGTGGCAAACATTGATTAAGATACCCCCTGTGAGTCCTTTCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTc                                                              >  1:436/1‑144 (MQ=255)                                                                           aTTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCg                                                             >  1:556816/1‑144 (MQ=255)                                                                           aTTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCg                                                             >  1:556817/1‑144 (MQ=255)                                                                                   gCGATATTGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAATGCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGc                                                     <  1:24726/144‑1 (MQ=255)                                                                                   gCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAAc                                                >  2:714584/1‑149 (MQ=255)                                                                                   gCGAGATGGCATTGATTGACTTGATGACCGCGCTCTGCATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTCACTTGTTGTACCAGGTCGGCTTTGGc                                                     <  1:312626/144‑1 (MQ=255)                                                                                         tGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCATTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATct                                          <  2:690658/149‑1 (MQ=255)                                                                                           gCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAAC‑GATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCAGCTTTGGCCCAACGAATctgc                                        >  2:717624/1‑149 (MQ=255)                                                                                               tgattgaCTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATctg                                         <  1:174990/144‑1 (MQ=255)                                                                                                    gaCTTGATGACCGCTCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGAt                                    <  1:325975/144‑1 (MQ=255)                                                                                                    gaCTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGAt                                    <  1:3022/144‑1 (MQ=255)                                                                                                      cTTGATGACCGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGaa                             >  2:977499/1‑149 (MQ=255)                                                                                                              ccGTCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTg                          <  1:650100/144‑1 (MQ=255)                                                                                                               cGCCCTCTGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTc                    >  2:680943/1‑149 (MQ=255)                                                                                                                gCCCTCTGGATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCa                        <  1:813852/144‑1 (MQ=255)                                                                                                                      tGTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTCAt                  <  1:537207/144‑1 (MQ=255)                                                                                                                       gTATGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTCAtt                 <  1:743825/144‑1 (MQ=255)                                                                                                                          tGTCTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTCATTGAt              <  1:1473/144‑1 (MQ=255)                                                                                                                             cTGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTAGCTATGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTCATTGATAAc           >  1:861909/1‑144 (MQ=255)                                                                                                                              tGCAACCAACT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTCATTGATAACATTACt     >  2:887977/1‑149 (MQ=255)                                                                                                                                caactaacT‑ATGTGGCAAATATTGATTAAGACACCCTCTTTAAGTCCTTGCTCTGTTTAAGCTTTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTCATTGATAACATTACTgg   <  2:723231/149‑1 (MQ=255)                                                                                                                                 aaccaacT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAATAATTGCAGGTCATTGATTACATTACTGGc  >  2:281858/1‑149 (MQ=255)                                                                                                                                   ccaacT‑ATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTTGCTCAACGAATCTGCTGATTAAAGAATTGCAGGTCATTGATACCATTACt     >  1:572980/1‑144 (MQ=255)                                                                                                                                         |                                                                                                                                              GTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTGTCAATTTATGAGCGATATGGCATTGATTGACTTGATGACCGCCCTCTGTATGTCTGCAACCAACTCATGTGGCAAACATTGATTAAGATACCCTCTGTAAGTCCTTGCTCTGTTTAATCTGTTTCGACTGACTTGTTGTACCAGGTCGGCTTTGGCCCAACGAATCTGCTGATCAAAGAATTGCAGGTCATTGATAACATTACTGGC  >  CP009273/3953301‑3953578

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑