Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	3,919,311	G→A	6.4%	S275S (AGC→AGT)	CJ019_03703 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	3,919,311	0	G	A	6.4%	206.3 / 3.5	64	S275S (AGC→AGT)	CJ019_03703	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (19/40);  new base A (2/2);  total (22/42)
Fisher's exact test for biased strand distribution p-value = 5.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.06e-01

TCATCGTGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTACATCGCCCTTGGCCAGCATATGGCCGCTGAATGCCC  >  KT2440/3919180‑3919441                                                                                                                                    |                                                                                                                                   tCATCGTGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTg                                                                                                                                 <  8:49863/135‑1 (MQ=255) tCATCGTGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTg                                                                                                                                 <  4:4858/135‑1 (MQ=255) tCATCGTGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGAGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTg                                                                                                                                 <  8:97863/135‑1 (MQ=255)   aTCGTGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGcc                                                                                                                               <  8:149260/135‑1 (MQ=255)   aTCGCGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGcc                                                                                                                               <  8:236313/135‑1 (MQ=255)    tCGTGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGcc                                                                                                                               <  4:326399/134‑1 (MQ=255)    tCGTGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGcc                                                                                                                               <  2:259186/134‑1 (MQ=255)       tGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGtt                                                                                                                            <  6:271246/134‑1 (MQ=255)       tGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGtt                                                                                                                            <  6:114939/134‑1 (MQ=255)       tGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTg                                                                                                                           <  6:207587/135‑1 (MQ=255)       tGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCATTGTACAGGATGGCCGAGCCGCTGCCGtt                                                                                                                            <  6:209147/134‑1 (MQ=255)                tCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGGAACCCCAACCATCAAAATTCCCCGCCCTTAATAAACGTTTTACAGGATGGCCGAGCCCCTTCCCTTGAACCGTGTa                                                                                                                  >  4:326331/1‑135 (MQ=255)                  gAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTAc                                                                                                                 <  7:68096/134‑1 (MQ=255)                         cGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGTCGCAGGTTGGCATCGCCAACGTTCAGATTGCGCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTTAACGGTGTACCGTCGGCg                                                                                                         <  3:143200/135‑1 (MQ=255)                          tgCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGt                                                                                                        <  1:73525/134‑1 (MQ=255)                          ggCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCTTTGAACGGTGTACCGTCGGCGt                                                                                                        <  7:59084/135‑1 (MQ=255)                          ggCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGt                                                                                                        <  5:59818/135‑1 (MQ=255)                          ggCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGt                                                                                                        <  6:181046/135‑1 (MQ=255)                          ggCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGt                                                                                                        <  6:130314/135‑1 (MQ=255)                                 cATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAgcgc                                                                                                  <  7:324225/134‑1 (MQ=255)                                        ccATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGa                                                                                            <  2:164712/133‑1 (MQ=255)                                        ccATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGAcc                                                                                          <  3:165445/135‑1 (MQ=255)                                        ccATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGAc                                                                                           <  6:238949/134‑1 (MQ=255)                                              aGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACCTTGCCCCGCCATTCATAACCGGTGTACAGGATGGCCGCGCCGCTGCCGTTGAACGGGGTACCGGCGGGGGTAGCGCCCGTGGccgggccc                                                                                    >  1:253930/1‑129 (MQ=255)                                               gcgcGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCt                                                                                   <  6:76187/135‑1 (MQ=255)                                               gcgcGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCt                                                                                   <  4:309980/135‑1 (MQ=255)                                                         cacCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGAGCTTGAAGGTATc                                                                         <  7:84950/135‑1 (MQ=255)                                                                    ggTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCgg                                                              <  6:37497/135‑1 (MQ=255)                                                                    ggTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCgg                                                              <  4:275357/135‑1 (MQ=255)                                                                      ttGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGcc                                                            <  2:274213/135‑1 (MQ=255)                                                                            tCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACg                                                      <  2:104958/135‑1 (MQ=255)                                                                            tCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACg                                                      <  8:116813/135‑1 (MQ=255)                                                                               ccAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCtc                                                   <  3:202486/135‑1 (MQ=255)                                                                               ccAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCtc                                                   <  3:45481/135‑1 (MQ=255)                                                                               ccAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCt                                                    <  3:45250/134‑1 (MQ=255)                                                                                 aaCCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCtcat                                                 <  1:41916/135‑1 (MQ=255)                                                                                  aCCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCtcatc                                                >  6:284210/1‑135 (MQ=255)                                                                                     ttCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCAcc                                             <  5:284210/135‑1 (MQ=255)                                                                                                 cGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAGCGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGCCCTTGAAGGTATCGCCCTCTCCGGCCGTGCCGGGCATCACCCCCCCTACAACg                                 >  3:21699/1‑135 (MQ=255)                                                                                                 cGCCATTCATAACCGTTGTACAGGATGGCCGAGCCACTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGa                                                                                            >  3:127081/1‑76 (MQ=255)                                                                                                 cGCCATTCATAACCGTTGTACAGGATGGCCGAGCCACTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGa                                                                                            >  3:121879/1‑76 (MQ=255)                                                                                                 cGCCATTCATAACCGTTGTACAGGATGGCCGAGCCACTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGa                                                                                            <  4:127081/76‑1 (MQ=255)                                                                                                 cGCCATTCATAACCGTTGTACAGGATGGCCGAGCCACTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGa                                                                                            <  4:121879/76‑1 (MQ=255)                                                                                                  gCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTa                                      >  8:69732/1‑129 (MQ=255)                                                                                                  gCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTa                                      <  7:69732/129‑1 (MQ=255)                                                                                                      ttCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTACATCGCCCtt                            <  8:262166/135‑1 (MQ=255)                                                                                                      ttCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTACATCGCCCtt                            <  5:283769/135‑1 (MQ=255)                                                                                                      agcATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTACATCGCCCtt                            <  7:68777/133‑1 (MQ=255)                                                                                                           aaCCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCCCGTACATCGCCCTTTGccc                       >  7:70158/1‑134 (MQ=255)                                                                                                                 tGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGCCCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGCCGCTCATCACCCCCCGTACATCGCCCATGGCCAGCatat                 >  6:333374/1‑135 (MQ=255)                                                                                                                   tACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTTAAGGTATAGCCCTCTCCGGCCGTGCCGCTCATCACCCCCCCTACAAACCCCTATGCCAGCattagg               >  6:37400/1‑131 (MQ=255)                                                                                                                    aCAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTa                                                                           >  7:298935/1‑74 (MQ=255)                                                                                                                    aCAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTa                                                                           <  8:298935/74‑1 (MQ=255)                                                                                                                    aCAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCGTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCGCATAACCCCCCGTACAAAGCCCATGGCCAGCAAATTGc              >  4:307485/1‑135 (MQ=255)                                                                                                                     cAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTACATCGCCCTTGGCCAGCCTATGGcc             >  7:110230/1‑135 (MQ=255)                                                                                                                      aGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGCCGCTCATCCCCCCACGTACATAGCCCATGGCCAGCCTATGGcct            >  8:68777/1‑134 (MQ=255)                                                                                                                      aGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGCCGCGCATCACCCCACGTACATCGCCCTTGGCCCGCATATGGCCg            >  2:43583/1‑135 (MQ=255)                                                                                                                           ggCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGCCGCGCAGCCCCCCCCGTACATAGCCCTTGGCCCGCCTATGGCCGcggca       >  1:68240/1‑131 (MQ=255)                                                                                                                           ggCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGGGTCGCTGATCACCCCCCCGACCTCGCCCATGGCCCGCAAATGGCCGCTgga       >  1:311382/1‑133 (MQ=255)                                                                                                                           ggCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATAGCCCTCTCCGGCCGTGACGCTCATCACCCCACCTACATCGCCCTTGGCCAGCATATGGCCGCTGaa       >  8:256658/1‑135 (MQ=255)                                                                                                                           ggCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCGTGAAGGTATCGCCCGCTCCGGCCGTGCCGGTGCTACCCCCACGTACATATCCCTTGGCCCGCATATGGGCGCTGaa       >  5:134984/1‑135 (MQ=255)                                                                                                                             ccGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGCAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTACATAGCCCTTGGCCAGCATATGGCCGCTGAATg     >  2:199939/1‑135 (MQ=255)                                                                                                                                aGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGCCCTCGCCCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCCTGACCCCCCGTACCTCCCCCTTGGCCCGCATATGGCCGCGGAATGgcc  >  2:82836/1‑135 (MQ=255)                                                                                                                                aGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGGCGCGCATAACCCCCCCGACCAAGCCCTTGGCCCGCAAATGGCCGCGGCAAGccc  >  5:324456/1‑135 (MQ=255)                                                                                                                                    |                                                                                                                                   TCATCGTGATCGGCTTCGAACATACGGCCTTTCATCTCGCCATCCAGCGCGGCGAACACCTGGCGCAGGTTGGCATCGCCAACCTTCACATTGCCCCGCCATTCATAACCGTTGTACAGGATGGCCGAGCCGCTGCCGTTGAACGGTGTACCGTCGGCGTAAGCGCCCTTGACCTCGACCTTGAAGGTATCGCCCTCTCCGGCCGTGACGCTCATCACCCCACGTACATCGCCCTTGGCCAGCATATGGCCGCTGAATGCCC  >  KT2440/3919180‑3919441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑