Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,068,231	A→G	11.7%	S51G (AGT→GGT)	ymdF →	conserved protein YmdF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,068,231	0	A	G	11.7%	76.9 / 2.4	38	S51G (AGT→GGT)	ymdF	conserved protein YmdF
Reads supporting (aligned to +/- strand):  ref base A (18/14);  new base G (2/2);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01

AGGCGGTTCCGGCAATTTTGCAGAAGACCGCGAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCT  >  NC_000913/1068095‑1068370                                                                                                                                         |                                                                                                                                            aGGCGGTTCCGGCAATTTTGCAGAAGACCGCGAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACg                                                                                                                                       >  1:743431/1‑143 (MQ=255) aGGCGGTGCCGGCAATTTTGCAGAAGACCGCGAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACg                                                                                                                                       <  1:390730/143‑1 (MQ=255)          cGGCAATTTTGCAGAAGACCGCGAAAGAGCATAAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATGTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGAAAAAGCg                                                                                                                              >  1:430388/1‑143 (MQ=255)           ggCAATTTTGCAGAAGACCGCGAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAATAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGa                                                                                                                             >  1:417287/1‑143 (MQ=255)                     cAGAAGACCGCGAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGAACCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAACAGTCACGGCAGAAGCGACAACTAGCCg                                                                                                                   >  2:694190/1‑143 (MQ=255)                      agaagaCCGCGAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACATCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGCCAAAACCGCCAACAAGCCgc                                                                                                                  >  2:406098/1‑142 (MQ=255)                        aagaCCGCGAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGc                                                                                                                >  1:338373/1‑143 (MQ=255)                             cgtgAAAGAGCATCAGAAGCAGGTAAAAACGTTGGACAGCTCAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATc                                                                                                           <  2:248879/140‑1 (MQ=255)                               cgAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTAACGGCAAAAGCGACAACTAGACGGGCTAACCaa                                                                                                         >  2:117487/1‑143 (MQ=255)                                gAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGTTAGGTCATGTGAGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAAt                                                                                                        <  1:518188/143‑1 (MQ=255)                                  aaGAGCAGCAGAAGGAGGTAAAAAGGGTGGACAGCACAGCGGGGGTAATTTCAAGAGTGTGCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGCGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGa                                                                                                      <  2:749345/143‑1 (MQ=255)                                      gCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGaa                                                                                                  <  1:388589/143‑1 (MQ=255)                                        aTCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCAGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAACGCGACAACTAGCCGGGCTAATCAATGACGAATg                                                                                                >  2:344150/1‑143 (MQ=255)                                              aGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCAtttt                                                                                          <  2:345340/143‑1 (MQ=255)                                                 aGGTAAAACAGGTGGACAGCATAGCGGGGGTAATGTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGt                                                                                       <  1:563826/143‑1 (MQ=255)                                                   gTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCGGTCACGGCAAAAGCGGGAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCt                                                                                     >  2:223034/1‑143 (MQ=255)                                                   gTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCGGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCt                                                                                     >  2:220258/1‑143 (MQ=255)                                                       actaGGTGGACAGCAGAGCGGGGGTAATTTCAGGAAGGGCCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGGAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAg                                                                                 <  2:17319/140‑1 (MQ=255)                                                            gTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCACTCACGAATGCATTTTTGTCTGTCGCTCGt                                                                            >  1:529854/1‑143 (MQ=255)                                                                   gcacagcGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGCACAGTCACGGCAAAAGCGACAACTAAACGGGCTAATCAATGACGAATGCATTTATGTCTGTAGCTCGTCAAAAAg                                                                     >  2:49224/1‑143 (MQ=255)                                                                     acagcGGGGGTCATTTCACGAATGACCCCCAGCGCGCATCTGGAGCAGGTAAAAAAGGTGGTAAGAGCAGACACGGCACACGAGTCTCCGAGCTGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGcc                                                                   <  1:141243/143‑1 (MQ=255)                                                                                  tttCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTCTCTGTCGCTCGTCACAAAGCCATCACCACCGCtt                                                      >  1:113590/1‑143 (MQ=255)                                                                                        gAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATAACCGCCGGTTAACCgg                                                >  2:360545/1‑143 (MQ=255)                                                                                            tgcccGCAGCCGGTATCGGGAGAAGGTAAAAAAGGTGGTAAGATCAGTCACGGCAAGAGCGTAATATAGCCTGGCTTCTCTCTGATTGTTGTTTTTTTGTCTGTAGGTCGTCAAAAAGCCATCGCCGCCGGTTACCCggtggt                                            <  2:336759/141‑1 (MQ=255)                                                                                               gcgcagcgcgcagcgGGAGGAGGGAAAAAAGGTGGGAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGa                                         <  1:637995/142‑1 (MQ=255)                                                                                                cGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGAt                                        >  1:745604/1‑143 (MQ=255)                                                                                                    gcgtgcAGCTGCAGCAGGTAAAAAAGGTGGTAATAGCAGTGTCGGCAACATCGACAACTAGCCGGGCTAACCAATGACGAATTCATTTTTGTCTGTAGTTCGTCAAAAAGCCATCACCGCCTGTTACCCGGTGGTTGATACtg                                    <  2:10462/143‑1 (MQ=255)                                                                                                                 ggagttAAAAAATGTGGTAAAGGCTGTCACGGCAAAAGCGACAAGTTTCCGGTTTAATCAATGACGAATGCATTGTTGTCGGTAGCGCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTaa                       <  1:316457/138‑1 (MQ=255)                                                                                                                 gCAGGTAAAAAAGGTTGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAAGGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTaa                       <  1:748064/143‑1 (MQ=255)                                                                                                                 gCAGGGAAAAAAGGTTGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATGTGTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTaa                       <  2:563469/143‑1 (MQ=255)                                                                                                                   aGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGATTACCCAGTGGTTGATACTAATGACAAATGTAAGc                     >  1:128533/1‑143 (MQ=255)                                                                                                                          aaaGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGACTGCGTGTTTGTCTGTAGCTCCCCAAAAAGCCATCACCGCCGGTTACCCGGAGGTCGATACTGCTGACACCTGCAACATTGCCTg              >  2:502823/1‑143 (MQ=255)                                                                                                                          aaaGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGAGACTGATGACAAATGTAAGCTTGCCTg              >  1:503103/1‑143 (MQ=255)                                                                                                                              gtggtAAGTGCGGTCACGGCAAAATCTGCTACTAGCCGGGCTAATCAATGACGAAAGCATTGTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgc          <  1:223034/143‑1 (MQ=255)                                                                                                                              gtggtAAGAGCGTTCACGGCTAATGCGACAACTAGCCGGGCGAAGCAATGACGAAGGCATTGTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgc          <  1:220258/143‑1 (MQ=255)                                                                                                                                   aaGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGTATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAACCTTGCCTGATGCGCGAt     >  2:105628/1‑143 (MQ=255)                                                                                                                                    agagCTGTCTCGCCACACACGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg    <  1:492975/143‑1 (MQ=255)                                                                                                                                      agCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGACGCt  >  2:527249/1‑143 (MQ=255)                                                                                                                                         |                                                                                                                                            AGGCGGTTCCGGCAATTTTGCAGAAGACCGCGAAAGAGCATCAGAAGCAGGTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCT  >  NC_000913/1068095‑1068370

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑