Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	2,236,631	T→A	5.6%	D140E (GAT→GAA)	sanA →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	2,236,631	0	T	A	5.6%	250.9 / 6.1	89	D140E (GAT→GAA)	sanA	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (52/32);  new base A (3/2);  total (55/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.79e-01

TCTCGATTACGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGATTCAGG  >  AP009048/2236562‑2236701                                                                      |                                                                       tctcGATTACGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGAtt                                                                       >  1:737166/1‑71 (MQ=255)  ctcGATTACGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGAttt                                                                      >  1:3809296/1‑71 (MQ=255)    cGATTACGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTc                                                                     >  1:4934427/1‑70 (MQ=255)     gATTACGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTc                                                                     <  1:3648190/69‑1 (MQ=255)     gATTACGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCat                                                                   >  1:167241/1‑71 (MQ=255)      aTTACGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCat                                                                   >  1:2498607/1‑70 (MQ=255)       ttgcGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCatta                                                                 >  1:2299427/4‑71 (MQ=255)          cGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCattatt                                                               <  1:351629/70‑1 (MQ=255)               gCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGAtt                                                                       <  1:3847212/57‑1 (MQ=255)                 tttCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCat                                                                   >  1:1145400/1‑59 (MQ=255)                 tttCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCAc                                                          <  1:3555148/68‑1 (MQ=255)                 tttCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACCAATGATTTCat                                                                   >  1:4346089/1‑59 (MQ=255)                  ttCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCaa                                                      >  1:2934706/1‑71 (MQ=255)                   tCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCAttatta                                                              >  1:211126/1‑62 (MQ=255)                   tCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCaa                                                      >  1:3042579/1‑70 (MQ=255)                   tCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCaa                                                      >  1:3321933/1‑70 (MQ=255)                     gTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACg                                                    <  1:3553250/70‑1 (MQ=255)                     gTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGt                                                   <  1:1992984/71‑1 (MQ=255)                      tACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGtt                                                  <  1:3662662/71‑1 (MQ=255)                        cGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTc                                                >  1:3785058/1‑71 (MQ=255)                        cGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTc                                                >  1:3416789/1‑71 (MQ=255)                            ggATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCatt                                                                  >  1:4669591/1‑49 (MQ=255)                            ggATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACt                                            >  1:380090/1‑71 (MQ=255)                             gATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCAc                                             <  1:5098769/69‑1 (MQ=255)                              aTTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTc                                                                     <  1:5006667/44‑1 (MQ=255)                              aTTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACtgt                                          <  1:332827/71‑1 (MQ=255)                               ttCCATCGTGCGTACACGCAAAGTTTTCGATAATAATGAAATCattag                                                                <  1:859845/48‑2 (MQ=25)                                 gcATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCAc                                                          >  1:3255517/2‑52 (MQ=255)                                 ccATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATtattat                                                             >  1:1730830/1‑49 (MQ=255)                                 ccATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATtattat                                                             >  1:5150500/1‑49 (MQ=255)                                 ccATCGTGCGTACACGCAAAGTTTTCGATAATAATGAAATCAttagta                                                              >  1:1309219/1‑48 (MQ=21)                                 ccATCGTGCGTACACGCAAAGTTTTCGATAATAATGAAATCAttagta                                                              >  1:4558997/1‑48 (MQ=21)                                  cATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCaa                                                      <  1:1658570/55‑1 (MQ=255)                                  cATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAAc                                                     >  1:5314368/1‑56 (MQ=255)                                  cATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAAc                                                     >  1:4219302/1‑56 (MQ=255)                                   aTCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCa                                              <  1:5040838/62‑1 (MQ=255)                                   aTCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTgagcg                                     <  1:3067432/71‑1 (MQ=255)                                    tCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCat                                                                   >  1:4650340/1‑40 (MQ=255)                                    tCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGttt                                                 >  1:154494/1‑58 (MQ=255)                                    tCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTgagc                                      >  1:3916784/1‑69 (MQ=255)                                    tCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTgagc                                      <  1:2697320/69‑1 (MQ=255)                                     cGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTgagcga                                    >  1:4419944/1‑70 (MQ=255)                                      gTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTgagcgag                                   <  1:1655580/70‑1 (MQ=255)                                      gTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTgagcgag                                   >  1:2911806/1‑70 (MQ=255)                                       tGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCa                                 <  1:5094749/71‑1 (MQ=255)                                           tACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCattat                             >  1:146318/1‑71 (MQ=255)                                            acacGCAAAGTTTTCGATACTAATGATTTCATTATTATc                                                            <  1:4076606/39‑1 (MQ=255)                                            acacGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACg                                                    >  1:1990005/1‑47 (MQ=255)                                            acacGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCa                                 >  1:4938358/1‑66 (MQ=255)                                             cacGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTcc                                               <  1:1642378/51‑1 (MQ=255)                                              acGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACg                                                    <  1:4600737/45‑1 (MQ=255)                                              acGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCAttattta                          >  1:3255511/1‑71 (MQ=255)                                              acGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCAttattta                          <  1:5006591/71‑1 (MQ=255)                                               cGCAAAGTTTTCGATACTAATGATTTCATTATTATc                                                            <  1:5308309/36‑1 (MQ=255)                                                gCAAAGTTTTCGATACTAATGATTTCATTATTATc                                                            >  1:1852001/1‑35 (MQ=255)                                                gCAAAGTTTTCGATACTAATGATTTCATTATTATCACGCAACGTTTCCACTGTgag                                       >  1:3914571/1‑56 (MQ=255)                                                 cAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTg                       >  1:2819981/1‑71 (MQ=255)                                                  aaaGTTTTCGATACTAATGATTTCATTATTATCACCCAACGt                                                   >  1:1627545/1‑42 (MQ=255)                                                  aaaGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTgc                      >  1:3668176/1‑71 (MQ=255)                                                  aaaGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTgc                      >  1:3505147/1‑71 (MQ=255)                                                  aaaGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTgc                      >  1:1455817/1‑71 (MQ=255)                                                  aaaGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTCTGAGCGAGCATTATTTATTgc                      >  1:379784/1‑71 (MQ=255)                                                      ttttCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTgcg                     <  1:1685108/68‑1 (MQ=255)                                                       tttCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCa                                 <  1:2105272/55‑1 (MQ=255)                                                        ttCGATACTAATGATTTCATTATTGTCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCa                >  1:4239496/1‑71 (MQ=255)                                                        ttCGATACTAATGATTTCATTATTATCACCCAACGTTTCCa                                              >  1:514011/1‑41 (MQ=255)                                                        ttCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACtgtg                                         <  1:3793535/46‑1 (MQ=255)                                                        ttCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCa                >  1:4331992/1‑71 (MQ=255)                                                        ttCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCa                >  1:4945291/1‑71 (MQ=255)                                                        ttCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCa                >  1:3071168/1‑71 (MQ=255)                                                        ttCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCa                >  1:4666938/1‑71 (MQ=255)                                                         tCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCa                <  1:4556391/70‑1 (MQ=255)                                                          cGATACTAATGATTTCATTATTATCACCCAACGTTTCCa                                              >  1:3065926/1‑39 (MQ=255)                                                           gATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCatat             <  1:2966655/71‑1 (MQ=255)                                                           gATAATAATGAAATCATTAGTATCACCCAACGTTTCCACTGTGAGCGAGCAttattta                          <  1:4589067/58‑1 (MQ=25)                                                            ataataATGAAATCATTAGTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGAGCTGCATATg            >  1:4146362/1‑71 (MQ=37)                                                            aTACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATg            <  1:894059/71‑1 (MQ=255)                                                             tACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTTAGCGAGCATTATTTATTGCGCTGCATATgg           <  1:691131/71‑1 (MQ=255)                                                             tACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCat                                >  1:1876033/1‑50 (MQ=255)                                                             tACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATgg           >  1:1934629/1‑71 (MQ=255)                                                               cTAATGATTTCATTATTATCACCCAACGTTTCCACTGTgagcga                                    <  1:1603541/44‑1 (MQ=255)                                                               cTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATggg          >  1:766623/1‑70 (MQ=255)                                                                tAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCatta                              <  1:1503897/49‑1 (MQ=255)                                                                 aaTGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGAt       >  1:2542942/1‑71 (MQ=255)                                                                  aTGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGAtt      <  1:3589995/71‑1 (MQ=255)                                                                  aTGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGAtt      >  1:2186796/1‑71 (MQ=255)                                                                   tGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGAtt      <  1:2241797/70‑1 (MQ=255)                                                                    gATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATgg           >  1:1298162/1‑64 (MQ=255)                                                                    gATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGAtt      >  1:4601380/1‑69 (MQ=255)                                                                    gATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGAtt      >  1:847510/1‑69 (MQ=255)                                                                     aTTTCATTATTATCACCCAACGTTTCCACTGTgagcga                                    >  1:3022766/1‑38 (MQ=255)                                                                     aTTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGATTCa    <  1:369990/70‑1 (MQ=255)                                                                      tttCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCAttattt                           <  1:3331870/46‑1 (MQ=255)                                                                      tttCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGATTCAgg  >  1:4547566/1‑71 (MQ=255)                                                                      |                                                                       TCTCGATTACGCAGGCTTTCGTACGCTGGATTCCATCGTGCGTACACGCAAAGTTTTCGATACTAATGATTTCATTATTATCACCCAACGTTTCCACTGTGAGCGAGCATTATTTATTGCGCTGCATATGGGGATTCAGG  >  AP009048/2236562‑2236701

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: ‑