Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,008,404	+G	coding (487/516 nt)	b4555 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,008,402	1	.	G	98.6%	220.6 / ‑3.3	69	coding (485/516 nt)	b4555	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base G (29/39);  total (29/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.16e-01

TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AA‑‑‑‑‑CT‑GGCTACAG‑CTGAAGGATTG‑ATTGCG‑‑TT‑‑GTGACGGGATGAACGACGCCGAAATGCTG  >  NC_000913/4008346‑4008458                                                                     |                                                               tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑tt                                 >  2:5367497/1‑93 (MQ=255) tCTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑tt                                 <  1:3067422/93‑1 (MQ=255)  cTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑ttt                                <  1:3423220/93‑2 (MQ=255)  cTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑ttt                                >  2:2607369/1‑92 (MQ=255)  cTGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑ttt                                >  2:2690426/1‑92 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑tttg                               >  2:1156237/1‑91 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑tttg                               >  2:4708075/1‑91 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑tttg                               >  1:5995372/1‑91 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑tttg                               >  1:5951006/1‑91 (MQ=255)   tGGAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑tttg                               <  1:1051706/93‑3 (MQ=255)    ggAAGTGATGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑tttgg                              >  2:630739/1‑90 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGa                      <  1:100493/93‑1 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGa                      <  2:5970655/93‑1 (MQ=255)            tGGCGGGCGGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGa                      <  2:349093/93‑1 (MQ=255)            tGGCGGGCGGCGTTTCAAAAAGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGa                      >  2:6045798/1‑93 (MQ=255)             ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGAt                     <  2:2148939/93‑1 (MQ=255)             ggcgggcgGCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑AAGAAACCG‑GGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGAt                     <  2:1686766/93‑1 (MQ=255)              gcgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATg                    <  2:2236559/93‑1 (MQ=255)              gcgggcggCGTGTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATg                    <  2:790947/93‑1 (MQ=255)               cgggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGa                   <  1:5478423/93‑1 (MQ=255)                gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGaa                  <  1:2635131/93‑1 (MQ=255)                gggcggCGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGaa                  <  2:3445771/93‑1 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAac                 <  1:4957056/93‑1 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAac                 <  2:331868/93‑1 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAac                 <  2:2772791/93‑1 (MQ=255)                 ggcggcGTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAac                 >  1:3993000/1‑93 (MQ=255)                  gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacg                >  1:4814006/1‑93 (MQ=255)                  gcggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacg                <  1:2957114/93‑1 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacga               <  1:2546223/93‑1 (MQ=255)                   cggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacga               <  2:2166732/93‑1 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTT‑‑GTGACGGGATGAacgac              >  2:5773184/1‑93 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacgac              >  2:5281397/1‑93 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacgac              >  2:3119511/1‑93 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacgac              <  2:4279944/93‑1 (MQ=255)                    ggcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacgac              <  2:4498313/93‑1 (MQ=255)                     gcgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAacgacg             >  2:4300379/1‑93 (MQ=255)                      cgTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGc            >  2:5938791/1‑93 (MQ=255)                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGcc           <  1:4418546/93‑1 (MQ=255)                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGcc           <  2:4808827/93‑1 (MQ=255)                         ttcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGa         <  2:2580522/89‑1 (MQ=255)                         ttcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGa         >  1:6270373/5‑93 (MQ=255)                         ttcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGa         >  2:5932837/5‑93 (MQ=255)                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaa        >  2:476989/4‑93 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaaa       <  2:723500/91‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaaa       <  2:808001/91‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaaa       <  1:3434171/91‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaaa       <  1:4553544/91‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaaa       >  1:4825533/3‑93 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaaa       <  1:995345/91‑1 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaaa       >  1:4825534/3‑93 (MQ=255)                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGaaa       <  1:5766444/91‑1 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAAt      >  2:3678743/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAAt      >  2:4130459/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAAt      >  2:1526869/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAAt      >  1:5825289/2‑93 (MQ=255)                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAAt      <  2:2946514/92‑1 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGCAATg     >  2:2085646/1‑93 (MQ=255)                             aaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATg     >  1:290367/1‑93 (MQ=255)                              aaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGc    <  1:6192030/93‑1 (MQ=255)                              aaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGc    >  2:3848605/1‑93 (MQ=255)                              aaGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGc    <  1:2935716/93‑1 (MQ=255)                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGCt   <  2:193059/93‑1 (MQ=255)                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGCt   <  1:3735094/93‑1 (MQ=255)                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGCt   >  2:6045723/1‑93 (MQ=255)                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGCt   <  1:1197056/93‑1 (MQ=255)                                ggCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGCTg  <  1:241840/93‑1 (MQ=255)                                ggCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGCTg  <  1:5385678/93‑1 (MQ=255)                                ggCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGCTg  <  1:4092752/93‑1 (MQ=255)                                ggCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCG‑‑TTTGGTGACGGGATGAACGACGCCGAAATGCTg  <  2:2269624/93‑1 (MQ=255)                                                                     |                                                               TCTGGAAGTGATGGCGGGCGGCGTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AA‑‑‑‑‑CT‑GGCTACAG‑CTGAAGGATTG‑ATTGCG‑‑TT‑‑GTGACGGGATGAACGACGCCGAAATGCTG  >  NC_000913/4008346‑4008458

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑