Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,601,044	C→A	31.0%	intergenic (+224/‑169)	prfC → / → osmY	peptide chain release factor RF‑3/periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,601,044	0	C	A	31.0%	24.1 / 17.1	26	intergenic (+224/‑169)	prfC/osmY	peptide chain release factor RF‑3/periplasmic protein
Reads supporting (aligned to +/- strand):  ref base C (10/8);  new base A (4/4);  total (14/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.79e-01

ATTCACTTTTGCTTATGTTTTCGCTGATATCCCGAGCGGTTTCAAAATTGTGATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGTCTCTCCCTATTCAGCAATGCAACCTCGTGTTGCCAGGCTCAAA  >  CP009273/4600902‑4601184                                                                                                                                               |                                                                                                                                             aTTCACTTTTGCTTATGTTTTCGCTGATATCCCGAGCGGTTTCAAAATTGTGATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTc                                                                                                                                              <  1:423229/143‑1 (MQ=255)              tATGTTTTCGCTGATATCCCGAGCGGTTTCAAAATTGTGATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGa                                                                                                                           >  2:610986/1‑149 (MQ=255)                   tttCGCTTAAATGCCAAGCGTTTTTAAAATTGTAATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTg                                                                                                                            <  1:220036/143‑1 (MQ=255)                        cTGAAATCCCGAGCGTGTTCAAAATTGTGATCTATATTTAACAAAGGTATGACATTTCTGACGGCGTTAAATACCGTTCAAGGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTATACCGATATTAATAACTGATTCa                                                                                                                       <  1:266792/143‑1 (MQ=255)                                ccGAGCGGTTTCAAAATTGTGATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTAATTCTACCGATATTAATAACTGATTCAGAGGCTGt                                                                                                               >  1:313351/1‑143 (MQ=255)                                         ttCAAAATTGTGATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATtca                                                                                                >  2:396365/1‑149 (MQ=255)                                          tCAAAATTGTGATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATtcat                                                                                               >  2:327066/1‑149 (MQ=255)                                               aTTGTGATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTATACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATtca                                                                                                <  1:452487/143‑1 (MQ=255)                                                     aTCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTATACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTc                                                                                          >  1:187118/1‑143 (MQ=255)                                                       cTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGCTATCCGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCGGTAATGGTCGTTATTCATCACTCATCGCttt                                                                                  >  2:486848/1‑149 (MQ=255)                                                            tttAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGa                                                                             >  2:606517/1‑149 (MQ=255)                                                                     gTGATGACATTTCTGACGGCGTTAAATACCGTTCCGTGAGTAGCTCCAAGTCGCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATgg                                                                          <  1:552594/143‑1 (MQ=255)                                                                             ttttCTGACGGCCTTAAAGACCGTTCAATGCGTAGATATCACTATCTAAATCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCTTCACTCTTCGCTTTAGTGATGGCGACCAtt                                                                  <  1:385672/142‑1 (MQ=255)                                                                             aTTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCAtt                                                                  <  1:349233/143‑1 (MQ=255)                                                                                     cGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAgg                                                    <  2:511672/149‑1 (MQ=255)                                                                                      ggCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTATACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTAATCACCACTCCCTTTTGTGATGGCGACCATTGACTTgtgt                                                         >  1:20790/1‑143 (MQ=255)                                                                                      ggCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTAATTATACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACACTTTAATTCTGTAGAgga                                                   >  2:504666/1‑148 (MQ=255)                                                                                         gTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTATACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATTGAGACCATTGACTTCTGTagc                                                      >  1:120247/1‑142 (MQ=255)                                                                                                aCCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGtctct                                         <  2:252082/149‑1 (MQ=255)                                                                                                       aaTGCGTAGATATCAGGAGCTAAAGCCGTCGATTGTCATTATACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGtctctc                                        <  1:284220/143‑1 (MQ=255)                                                                                                          gCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGTCTCTCCCt                                     <  1:375987/143‑1 (MQ=255)                                                                                                           cGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGTCTCTcccca                                    >  1:229146/1‑141 (MQ=255)                                                                                                            gTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATGAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGTCTCTCCCTATTCAGCa                             <  2:356963/149‑1 (MQ=255)                                                                                                              aGATATCAGTATCTAAAGCCGTCGATTGTCATTATACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGTCTCTCCCTATTCAGCAAt                           <  2:210225/149‑1 (MQ=255)                                                                                                                         tCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGAGAGCATTCACTTCTGTAGAGGGTGAAGGCTCGACCTATTAAGCAATGCAAc                      >  1:89918/1‑143 (MQ=255)                                                                                                                                   tCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGTCTCTCCCTATTCAGCAATGCAACCTCGTGTTGCCAGGCt      >  2:574044/1‑149 (MQ=255)                                                                                                                                             ttCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGTCTCTCCCTATTCAGCAATGCAACCTCGTGTTGCCAGGCTCaaa  >  1:303005/1‑143 (MQ=255)                                                                                                                                               |                                                                                                                                             ATTCACTTTTGCTTATGTTTTCGCTGATATCCCGAGCGGTTTCAAAATTGTGATCTATATTTAACAAAGTGATGACATTTCTGACGGCGTTAAATACCGTTCAATGCGTAGATATCAGTATCTAAAGCCGTCGATTGTCATTCTACCGATATTAATAACTGATTCAGAGGCTGTAATGGTCGTTATTCATCACTCATCGCTTTTGTGATGGCGACCATTGACTTCTGTAGAGGGTGAAGTCTCTCCCTATTCAGCAATGCAACCTCGTGTTGCCAGGCTCAAA  >  CP009273/4600902‑4601184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑