Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	4,409,322	0	G	A	55.4%	18.9 / 86.3	65	intergenic (‑29/‑121)	CJ019_04171/CJ019_04172	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (11/18);  new base A (16/20);  total (27/38)
Fisher's exact test for biased strand distribution p-value = 6.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GATATGGCGGTATCCAAGCCCACCCAGCAGCGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATGCATACAGTAAATGGAGCGCTACCACCGTGTCTAAAGC  >  KT2440/4409189‑4409453                                                                                                                                      |                                                                                                                                    gATATGGCGGTATCCAAGCCCACCCAGCAGCGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGt                                                                                                                                    <  6:222368/135‑1 (MQ=255)   tatGGCGGTATCCAAGCCCACCCAGCAGCGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTCGGCTCCTTACCTGCGACTAATTTTAGTTGc                                                                                                                                 >  7:180261/1‑136 (MQ=255)                     cacccaGCAGCGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCaa                                                                                                               <  1:11656/136‑1 (MQ=255)                       cccaGCAGCGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGATCAGCTTTTCTTTCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATc                                                                                                             <  2:245742/136‑1 (MQ=255)                         cagcagCGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTc                                                                                                                 >  1:205462/1‑130 (MQ=255)                         cagcagCGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTc                                                                                                                 <  2:205462/130‑1 (MQ=255)                          agcagcGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCATCAGCTTCGCGAGCAGCTTTTCTTGATTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATTACAGGTCAATCAt                                                                                                           >  7:192827/1‑135 (MQ=255)                          agcagcGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCAtt                                                                                                          >  8:216834/1‑136 (MQ=255)                          agcagcGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCAt                                                                                                           >  5:47817/1‑135 (MQ=255)                            cagcGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTcc                                                                                                        <  3:139287/136‑1 (MQ=255)                               cGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGt                                                                                                     <  2:30866/136‑1 (MQ=255)                               cGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGt                                                                                                     <  4:70224/136‑1 (MQ=255)                                gTGACCATCTCAGGCATAGTGACTCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGTCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGtt                                                                                                    <  3:35251/136‑1 (MQ=255)                                     cAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGCCTAATTTTAATTGAGATTCTATGACAGGTCAATCATTCCACTTAGGAg                                                                                               >  8:97240/1‑136 (MQ=255)                                     cAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAg                                                                                               >  5:90039/1‑136 (MQ=255)                                     cAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAg                                                                                               >  5:86032/1‑136 (MQ=255)                                     cAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTAAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCTACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAg                                                                                               >  2:79432/1‑136 (MQ=255)                                           aGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGc                                                                                                                            >  2:209930/1‑101 (MQ=255)                                           aGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGc                                                                                                                            <  1:209930/101‑1 (MQ=255)                                           aGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACa                                                                                           <  1:119051/134‑1 (MQ=255)                                            ggCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAAt                                                                                        <  6:191004/136‑1 (MQ=255)                                              ccAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAAtgt                                                                                      <  7:73472/136‑1 (MQ=255)                                              ccAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAAtgt                                                                                      <  7:18290/136‑1 (MQ=255)                                               cAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAAtgtg                                                                                     <  7:216834/136‑1 (MQ=255)                                                   tGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGctct                                                                                 <  7:168214/136‑1 (MQ=255)                                                   tGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGctct                                                                                 <  5:196202/136‑1 (MQ=255)                                                     aaTCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTAt                                                                               >  1:11538/1‑136 (MQ=255)                                                          ttcttgcttgTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAg                                                                           >  7:4743/3‑135 (MQ=255)                                                          tgcttgctTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCa                                                                                                       <  4:167030/107‑1 (MQ=255)                                                          tgcttgctTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCa                                                                                                       >  3:167030/1‑107 (MQ=255)                                                          tgcttgctTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAg                                                                           >  7:155645/1‑135 (MQ=255)                                                          tgcttgctTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAg                                                                           >  3:173644/1‑135 (MQ=255)                                                            cttgcttgTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTAt                                                                        <  3:244950/136‑1 (MQ=255)                                                               gcttgTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGc                                                                     >  2:1899/1‑136 (MQ=255)                                                               gcttgTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGt                                                                                                     <  4:30679/104‑1 (MQ=255)                                                               gcttgTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGt                                                                                                     >  3:30679/1‑104 (MQ=255)                                                               gcttgTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGc                                                                     >  5:87995/1‑136 (MQ=255)                                                                       agcagcTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             <  6:90039/136‑1 (MQ=255)                                                                       agcagcTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             <  6:86032/136‑1 (MQ=255)                                                                       agcagcTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             <  7:97240/136‑1 (MQ=255)                                                                       agcagcTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             <  7:246638/136‑1 (MQ=255)                                                                       agcagcTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             <  1:79432/136‑1 (MQ=255)                                                                       agcagcTTCGCGAGCAGCGTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             <  1:101061/136‑1 (MQ=255)                                                                       agcagcTTCGAGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             <  8:192827/136‑1 (MQ=255)                                                                               cgcgAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCa                                                                            <  8:61293/113‑1 (MQ=255)                                                                               cgcgAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCa                                                                            >  7:61293/1‑113 (MQ=255)                                                                                gcgAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATa                                                     <  6:221201/135‑1 (MQ=255)                                                                                 cgAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATaaa                                                   <  8:155645/136‑1 (MQ=255)                                                                                 cgAGCAGCGTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATaa                                                    >  8:11961/1‑135 (MQ=255)                                                                                    gcagcTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATa                                                <  5:58095/136‑1 (MQ=255)                                                                                       gcTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTg                                             <  6:47817/136‑1 (MQ=255)                                                                                                gCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATg                                       <  2:166353/133‑1 (MQ=255)                                                                                                gCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATg                                       <  8:53090/133‑1 (MQ=255)                                                                                                gCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATg                                       <  8:180261/133‑1 (MQ=255)                                                                                                gCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATg                                       <  4:82434/133‑1 (MQ=255)                                                                                                                   ttACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCa                                                                                                            >  4:193196/1‑45 (MQ=255)                                                                                                                   ttACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCa                                                                                                            <  3:193196/45‑1 (MQ=255)                                                                                                                    tACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             <  1:234501/91‑1 (MQ=255)                                                                                                                    tACCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACt                                                             >  2:234501/1‑91 (MQ=255)                                                                                                                     aCCTGCGACTAATTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATGCATACAGTAAATGGAGCGCTacca               >  1:3725/1‑136 (MQ=255)                                                                                                                               aaTTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATGCATACAGTAAATGGAGCGCTCCCACCGTGTCTa      >  5:133461/1‑135 (MQ=255)                                                                                                                               aaTTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATGCATACAGTAAATGGAGCGCTACCACCgtgt         >  6:17667/1‑132 (MQ=255)                                                                                                                               aaTTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATGCATACAGTAAATGGAGCGCTACCACCgtgt         <  5:17667/132‑1 (MQ=255)                                                                                                                               aaTTTTAATTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATGCATACAGTAAATGGAGCGCTACCACCGTGTCTa      >  3:63130/1‑135 (MQ=255)                                                                                                                                   ttAATTGCGATGGTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATGCATACAGTAAATGGAGCGCTACCACCGTGTCTAAAGc  >  5:143174/1‑135 (MQ=255)                                                                                                                                      |                                                                                                                                    GATATGGCGGTATCCAAGCCCACCCAGCAGCGTGACCAGCTCAGGCCAAGTGAATCCTGCTTGCTTGTTCAGCAGCTTCGCGAGCAGCTTTTCTTGCTTAGACATTTGGGCTCCTTACCTGCGACTAATTTTAGTTGCGATGCTATGACAGGTCAATCATTCCAGTTAGGAGTACAAATGTGCTCTATCCAGTATTGCCATTTACTGGCAGATAAAATACTGTCTATGCATACAGTAAATGGAGCGCTACCACCGTGTCTAAAGC  >  KT2440/4409189‑4409453

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑