Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	1,590,693	A→G	8.9%	L341L (CTT→CTC)	ydeT ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	1,590,693	0	A	G	8.9%	152.1 / 6.8	56	L341L (CTT→CTC)	ydeT	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (27/24);  new base G (3/2);  total (30/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

TCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATTCTCTCCGTGTGTGAC  >  AP009048/1590631‑1590761                                                               |                                                                     tCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAg                                                                    <  1:455514/65‑1 (MQ=255) tCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGt                                                                   >  1:1997710/1‑66 (MQ=255)  cGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGt                                                              >  1:2140803/1‑70 (MQ=255)   gACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGt                                                              <  1:674002/69‑1 (MQ=255)   gACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGt                                                              >  1:4597645/1‑69 (MQ=255)   gACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGt                                                              >  1:2219796/1‑69 (MQ=255)    aCAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGGAGTCCAGTCAg                                                           <  1:748488/71‑1 (MQ=255)       aTACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATa                                                        <  1:2849431/71‑1 (MQ=255)         aCAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGa                                                          >  1:3161718/1‑67 (MQ=255)          cAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATaaa                                                      <  1:1128758/70‑1 (MQ=255)          cAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAAc                                                     >  1:1876200/1‑71 (MQ=255)          cAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCAAGTCAGATAAAc                                                     >  1:3662980/1‑71 (MQ=255)            gTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCt                                                   <  1:1643533/71‑1 (MQ=255)                  gTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCAt                                             >  1:1283677/1‑71 (MQ=255)                     tttATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGt                                                                   <  1:3899200/46‑1 (MQ=255)                      ttATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTc                                         >  1:377559/1‑71 (MQ=255)                       tATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTcc                                        >  1:1122581/1‑71 (MQ=255)                         tCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTcc                                        <  1:2291370/69‑1 (MQ=255)                          cTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATaa                                                       <  1:1332934/53‑1 (MQ=255)                          cTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCcgc                                      >  1:1602178/1‑70 (MQ=255)                           tttGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGta                                                                  >  1:2117298/1‑40 (MQ=255)                             tGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCcgc                                      <  1:3542703/67‑1 (MQ=255)                              gCCCCATGAAACCTTTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGAc                                   <  1:2215982/69‑1 (MQ=255)                              gCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACaa                                 >  1:70861/1‑71 (MQ=255)                              gCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACa                                  <  1:248537/70‑1 (MQ=255)                              gCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACa                                  <  1:1168804/70‑1 (MQ=255)                               ccccATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGt                                                              <  1:2190374/41‑1 (MQ=255)                                  cATGAAACCTGTAATTGCCCTGACTGTGGGAGTCCAGTCAGATAAACCt                                                   <  1:3708129/49‑1 (MQ=255)                                  cATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACaa                                 >  1:2668255/1‑67 (MQ=255)                                  cATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAAtgct                             >  1:3257545/1‑71 (MQ=255)                                    tGAAACCTGTAATTGCCCTGACTGTGGGAGTCCAGTCAGATAAACCTGa                                                 >  1:2314379/1‑49 (MQ=255)                                    tGAAACCTGTAATTGCCCTGACTGTGGGAGTCCAGTCAGATAAACCTGa                                                 >  1:3604718/1‑49 (MQ=255)                                    tGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCcgcg                                     <  1:4565544/61‑1 (MQ=255)                                    tGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAAtgctgc                           >  1:2838328/1‑71 (MQ=255)                                     gAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGt                                                              >  1:65424/1‑35 (MQ=255)                                     gAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCt                                                   <  1:1399398/46‑1 (MQ=255)                                      aaaCCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATaa                                                       <  1:3927598/41‑1 (MQ=255)                                      aaaCCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGa                                                 >  1:2078704/1‑47 (MQ=255)                                      aaaCCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCa                         >  1:1203024/1‑71 (MQ=255)                                         ccTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCAttt                      <  1:4529325/71‑1 (MQ=255)                                          cTGTAATTGCCCTGACTGTGGGAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGGCAtttt                     >  1:3157845/1‑71 (MQ=255)                                            gTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTa                   >  1:1902495/1‑71 (MQ=255)                                             tAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTAt                  >  1:1807285/1‑71 (MQ=255)                                               aTTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATtc                >  1:2109137/1‑71 (MQ=255)                                                ttGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAAtg                               <  1:4148631/55‑1 (MQ=255)                                                ttGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATtct               <  1:2708958/71‑1 (MQ=255)                                                  gCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACaa                                 >  1:2545146/1‑51 (MQ=255)                                                    ccTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATTATCTcc           <  1:2194694/71‑1 (MQ=255)                                                       gACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACa                                  <  1:2217438/45‑1 (MQ=255)                                                       gACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACa                                  <  1:1166292/45‑1 (MQ=255)                                                       gACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATTCTCTCCgtg        >  1:2377440/1‑71 (MQ=255)                                                         cTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCAtttt                     >  1:723661/1‑56 (MQ=255)                                                          tgtgGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGAc                                   <  1:1529191/41‑1 (MQ=255)                                                             ggAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATTCTCTCCGTGTGTGa   >  1:3392584/1‑70 (MQ=255)                                                              gAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATTCTCTCCGTGTGTGAc  >  1:4410934/1‑70 (MQ=255)                                                              gAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATTCTCTCCGTGTGTGAc  <  1:652684/70‑1 (MQ=255)                                                               |                                                                     TCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTAATTGCCCTGACTGTGGAAGTCCAGTCAGATAAACCTGACCATTTTCCGCGACAATGCTGCCATTTTTATTCTCTCCGTGTGTGAC  >  AP009048/1590631‑1590761

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑