Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	4,123,873	G→A	8.0%	R255H (CGC→CAC)	damX →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	4,123,873	0	G	A	8.0%	277.1 / 9.9	87	R255H (CGC→CAC)	damX	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (42/38);  new base A (3/4);  total (45/42)
Fisher's exact test for biased strand distribution p-value = 7.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

CCTGTTCGCAATGGCAATGCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGAAAACGGAGCCGAAGC  >  AP009048/4123803‑4123941                                                                       |                                                                     ccTGTTCGCAATGGCAATGCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTAcgcg                                                                      <  1:3029941/71‑1 (MQ=255)      tCGCAATGGCAATGCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTAcgcg                                                                      >  1:4280167/1‑66 (MQ=255)      tCGCAATGGCAATGCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAg                                                                 >  1:3189760/1‑71 (MQ=255)      tCGCAATGGCAATGCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAg                                                                 >  1:351755/1‑71 (MQ=255)      tCGCAATGGCAATGCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAg                                                                 >  1:2162838/1‑71 (MQ=255)        gcaatggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGc                                                                <  1:1579571/70‑1 (MQ=255)        gcaatggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCt                                                               >  1:4014738/1‑71 (MQ=255)         caatggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTc                                                              <  1:2158962/71‑1 (MQ=255)          aatggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCg                                                             >  1:3448956/1‑71 (MQ=255)          aatggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCg                                                             <  1:1976796/71‑1 (MQ=255)          aatggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCg                                                             <  1:1790487/71‑1 (MQ=255)           atggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGt                                                            <  1:1303268/71‑1 (MQ=255)           acggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGt                                                            <  1:2375923/69‑1 (MQ=255)            tggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGt                                                            >  1:902328/1‑70 (MQ=255)            tggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGt                                                            >  1:2699338/1‑70 (MQ=255)            tggcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTc                                                           <  1:2058234/71‑1 (MQ=255)              gcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTca                                                          <  1:3796139/70‑1 (MQ=255)              gcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTca                                                          <  1:305234/70‑1 (MQ=255)              gcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCACCCAGCTCGTcag                                                         >  1:2264997/1‑71 (MQ=255)              gcaatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCACCCAGCTCGTcag                                                         <  1:4398289/71‑1 (MQ=255)               caatgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGc                                                                <  1:1247935/63‑1 (MQ=255)                 atgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTcagcag                                                      <  1:3903165/71‑1 (MQ=255)                  tgCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAgg                                                     >  1:4287336/1‑71 (MQ=255)                   gCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGt                                                            <  1:2778350/63‑1 (MQ=255)                   gCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCAAGCt                                                               >  1:4022680/1‑60 (MQ=255)                    cATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCg                                                   >  1:3693089/1‑71 (MQ=255)                     aTCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCgg                                                  >  1:3827850/1‑71 (MQ=255)                      tCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGt                                                 <  1:949881/71‑1 (MQ=255)                      tCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGt                                                 >  1:3815648/1‑71 (MQ=255)                      tCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGt                                                 <  1:3771821/71‑1 (MQ=255)                      tCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGt                                                 >  1:1999517/1‑71 (MQ=255)                      tCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCACCCAGCTCGTCAGCAGGCGGt                                                 <  1:1314071/71‑1 (MQ=255)                       cgcgTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGt                                                 >  1:3291024/1‑70 (MQ=255)                       cgcgTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGt                                                 >  1:1359019/1‑70 (MQ=255)                       cgcgTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGt                                                 >  1:4329405/1‑70 (MQ=255)                       cgcgTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGt                                                 >  1:1808905/1‑70 (MQ=255)                        gcgTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTg                                                <  1:2300265/70‑1 (MQ=255)                        gcgTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTg                                                <  1:2827398/70‑1 (MQ=255)                          gTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGcc                                                                    >  1:1207855/1‑48 (MQ=255)                           tGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCg                                                   <  1:3313252/64‑1 (MQ=255)                           tGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCACCCAGCTCGTcag                                                         <  1:155880/58‑1 (MQ=255)                            gACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTca                                                          >  1:141624/1‑56 (MQ=255)                             acacGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGa                                           <  1:765555/70‑1 (MQ=255)                               acGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAAcc                                        >  1:3429978/1‑71 (MQ=255)                                  gCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaa                                     <  1:2686652/71‑1 (MQ=255)                                  gCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCACCCAGCTCGTCAGCAGGCGGTGATTGAACCGa                                      <  1:1407863/70‑1 (MQ=255)                                    gAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGAt                                              >  1:1927555/1‑60 (MQ=255)                                    gAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaa                                   <  1:28305/71‑1 (MQ=255)                                    gAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaa                                   <  1:4195141/71‑1 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGAtt                                             >  1:972875/1‑59 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaaaa                                 >  1:305967/1‑71 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaaaa                                 >  1:1930880/1‑71 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaaaa                                 >  1:3973428/1‑71 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaaaa                                 <  1:4276156/71‑1 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaaaa                                 >  1:1229945/1‑71 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaaaa                                 >  1:2410029/1‑71 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGaaaaaa                                 <  1:1243397/71‑1 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGGCAGCAGGCGGTGATTGAACCGaaaaaa                                 <  1:2533404/71‑1 (MQ=255)                                      aaaCGCAAACCGCTGAACGTCCGTCCACTACGCACCCAGCTCGTCAGCAGGCGGTGATTGAAc                                         >  1:1541179/1‑63 (MQ=255)                                       aaCGCAAACCGCTGAACGTCCGTCCACTACGCACCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAAc                                >  1:3919454/1‑71 (MQ=255)                                        aCGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGt                                                            >  1:2980817/1‑42 (MQ=255)                                          gCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCgc                             <  1:3055634/71‑1 (MQ=255)                                           cAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCgca                            <  1:2001437/71‑1 (MQ=255)                                           cAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCgc                             >  1:3114129/1‑70 (MQ=255)                                              aCCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGt                                                            >  1:4125954/1‑36 (MQ=255)                                              aCCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGt                                                            >  1:4272068/1‑36 (MQ=255)                                               ccGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCgcaagca                        <  1:2485093/71‑1 (MQ=255)                                               ccGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCgcaagc                         >  1:2817935/1‑70 (MQ=255)                                                 gCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGaa                                          >  1:3292503/1‑51 (MQ=255)                                                 gCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGaa                                          >  1:4509807/1‑51 (MQ=255)                                                  cTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAAcc                     <  1:3953389/71‑1 (MQ=255)                                                   tGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCg                    >  1:1588368/1‑71 (MQ=255)                                                    gAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCgcaa                           >  1:827100/1‑63 (MQ=255)                                                    gAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGt                   >  1:3652585/1‑71 (MQ=255)                                                     aaCGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTg                  <  1:2138311/71‑1 (MQ=255)                                                      aCGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAAcc                               >  1:3984100/1‑57 (MQ=255)                                                      aCGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCgc                             <  1:2093184/59‑1 (MQ=255)                                                       cgtccgtcCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGaa                <  1:1006075/71‑1 (MQ=255)                                                        gtccgtccACTACGCGCCCAGCTCGTCAGCAGG‑GGTGATTGAACCGAAAAAACCGCAAGCAACCGTGaaaa              <  1:1437525/71‑1 (MQ=255)                                                         tacgtccACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGaaaa              <  1:2232865/69‑1 (MQ=255)                                                           cgtccACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGAAAAc             <  1:3347521/70‑1 (MQ=255)                                                           cgtccACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGAAAACg            >  1:3466024/1‑71 (MQ=255)                                                            gtccACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGAAAACgg           <  1:2684536/71‑1 (MQ=255)                                                             tccACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCgcaa                           >  1:3553471/1‑54 (MQ=255)                                                             tccACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGAAAACg            >  1:4406050/1‑69 (MQ=255)                                                               cACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCg                                       <  1:159222/40‑1 (MQ=255)                                                                 cTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGaa                <  1:1038461/61‑1 (MQ=255)                                                                 cTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGAAAACGGAGCCg      <  1:4068061/71‑1 (MQ=255)                                                                   aCGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAAACGCAAGCAACCGTGAAAACGGAGCCg      >  1:4385948/1‑69 (MQ=255)                                                                     gcgcCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGaaaa              <  1:1848072/59‑1 (MQ=255)                                                                     gcgcCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGaaaa              <  1:2451817/59‑1 (MQ=255)                                                                     gcgcCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGAAAACGGAGCCGAAGc  <  1:4243717/71‑1 (MQ=255)                                                                       |                                                                     CCTGTTCGCAATGGCAATGCATCGCGTGACACGGCGAAAACGCAAACCGCTGAACGTCCGTCCACTACGCGCCCAGCTCGTCAGCAGGCGGTGATTGAACCGAAAAAACCGCAAGCAACCGTGAAAACGGAGCCGAAGC  >  AP009048/4123803‑4123941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑