Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,752,380	C→A	15.4%	P13T (CCT→ACT)	yfjI →	CP4‑57 prophage; uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,752,380	0	C	A	15.4%	71.8 / 2.6	26	P13T (CCT→ACT)	yfjI	CP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (13/9);  new base A (2/2);  total (15/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.04e-01

TTGAGGCCGAGATTGATGAGTGGTTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGATAAACTGCTGATGAAGCCATTATATCAACTGGAAGAGGATTTATTTGAA  >  CP009273/2752166‑2752631                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                            ttGAGGCCGAGATTGATGAGTGGTTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTca                                                                                                                                                                                                                                                            <  2:55432/216‑2 (MQ=255)                          aTCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAg                                                                                                                                                                                                                               >  1:181075/1‑220 (MQ=255)                              caACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGa                                                                                                                                                                                                                           <  2:181069/220‑1 (MQ=255)                                                                                              aaaCATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATAc                                                                                                                                                                                                                  >  2:26182/1‑165 (MQ=255)                                                                                                  aTCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAg                                                                                                                                                                                                              <  1:26183/165‑1 (MQ=255)                                                                                                                                           gCTAAACAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATc                                                                                                                                                                                                                                                  >  2:397075/1‑88 (MQ=255)                                                                                                                                               aaCAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGa                                                                                                                                                                                                                                              <  1:397088/88‑1 (MQ=255)                                                                                                                                                                              aTTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTTGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGATAAAAANCTGATGAAGACaagagatgacatg                    >  2:294395/1‑263 (MQ=255)                                                                                                                                                                                  cATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGATAAACTGCTGATGAAGCCATTATATCAACTGGa                  <  1:294403/273‑1 (MQ=255)                                                                                                                                                                                          aTGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTa                                                                                                        >  1:439017/1‑179 (MQ=255)                                                                                                                                                                                              tcgtcCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCAc                                                                                                    <  2:439004/179‑1 (MQ=255)                                                                                                                                                                                                gtcCTTTCCCTGTAGATGCATTTCCTAAAATTATCAgg                                                                                                                                                                                                                                               >  1:190564/1‑38 (MQ=255)                                                                                                                                                                                                gtcCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGTCTGAATCAGGTGAACGTAAGAGTACGGTTGATAAACTGCTGATGAAGCCATTATATCAACTGGAAGAGGATTTATTTGaa  >  1:234028/1‑275 (MQ=255)                                                                                                                                                                                                 tcCTTTCCCTGTAGATGCATTTCCTACAATTATCCGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGACCGGTATCACTTTTCTTNATGACTCTNGCTGAATCAGGTTAACGTAAGAGTACGGTTGATAAACTGCTGATGAAGCCATTATATCAACTGGAAGAGGATTTATTTGaa  >  1:332047/1‑274 (MQ=255)                                                                                                                                                                                                   cTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGccc                                                                                                                                                                                                          >  1:307062/1‑72 (MQ=255)                                                                                                                                                                                                    tttCCCTGTAGATGCATTTCCTAAAATTATCAGGAATg                                                                                                                                                                                                                                           <  2:190558/38‑1 (MQ=255)                                                                                                                                                                                                     ttCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAag                                                              >  1:311957/1‑210 (MQ=255)                                                                                                                                                                                                       cccTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCa                                                                                                                                                                                                      <  2:307053/72‑1 (MQ=255)                                                                                                                                                                                                         cTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTa                                                          <  2:311948/210‑1 (MQ=255)                                                                                                                                                                                                            tAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTAc                                                                                                                   >  2:410387/1‑150 (MQ=255)                                                                                                                                                                                                            tAGATGCATTTACTAAAATTATCAGGAATGCAATTTAt                                                                                                                                                                                                                                   >  2:273699/1‑38 (MQ=255)                                                                                                                                                                                                               aTGCATTTACTAAAATTATCAGGAATGCAATTTATGAAg                                                                                                                                                                                                                               >  2:457079/1‑39 (MQ=255)                                                                                                                                                                                                                tGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTgg                                                                                                               <  1:410400/150‑1 (MQ=255)                                                                                                                                                                                                                tGCATTTACTAAAATTATCAGGAATGCAATTTATGAAg                                                                                                                                                                                                                               <  1:273707/38‑1 (MQ=255)                                                                                                                                                                                                                   aTTTACTAAAATTATCAGGAATGCAATTTATGAAGTGGa                                                                                                                                                                                                                           <  1:457092/39‑1 (MQ=255)                                                                                                                                                                                                                    tttCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATtgctg                                                                                                                                                                                        >  2:256648/1‑73 (MQ=255)                                                                                                                                                                                                                      tCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCt                                                                                >  2:214967/1‑175 (MQ=255)                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                            TTGAGGCCGAGATTGATGAGTGGTTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAATTTAATTAAATAAGAGGCATTGCATGTTCAATGGTCGTCCTTTCCCTGTAGATGCATTTCCTAAAATTATCAGGAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGATAAACTGCTGATGAAGCCATTATATCAACTGGAAGAGGATTTATTTGAA  >  CP009273/2752166‑2752631

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑