Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	1,348,440	0	C	G	29.5%	76.1 / 11.2	44	intergenic (‑11/+129)	CJ019_01261/CJ019_01262	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (6/25);  new base G (13/0);  total (19/25)
Fisher's exact test for biased strand distribution p-value = 5.23e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CGACAGTGCCGTTACGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATCCGCCCGCGCGGGCGTACCGACTTCGGGACAGACTCAGGA  >  KT2440/1348306‑1348574                                                                                                                                       |                                                                                                                                       cgacAGTGCCGTTACGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATGCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGtctc                                                                                                                                      <  1:43684/137‑1 (MQ=255) cgacAGTGCCGTTACGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGtctc                                                                                                                                      <  4:33417/137‑1 (MQ=255) cgacAGTGCCGTTACGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGtctc                                                                                                                                      <  3:146794/137‑1 (MQ=255)         ccGTTACGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGGGGGTTTGGTTGGGTGGGGGTGTCGACAGttt                                                                                                                              >  3:67343/1‑137 (MQ=255)               cGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTGGGTTTTGATGGGTGGGTGTGGGCACAGTttatttat                                                                                                                        >  7:247916/1‑137 (MQ=255)               cGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTGGGTTTGCATGGGTGGGTGTCTACCCACtttgttttt                                                                                                                        >  7:38719/1‑131 (MQ=255)               cGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGGCGGGTTGGAATGGTTGGGGTCACCAAAGTTTatatat                                                                                                                        >  2:336325/1‑137 (MQ=255)                 cTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTAGGTTTGCTTTGGTGGGAGTGTCCAAAGTTTTTATAttt                                                                                                                      >  2:342059/1‑136 (MQ=255)                    gATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTGCACCGTTTCTATATTGtta                                                                                                                   >  8:348901/1‑136 (MQ=255)                    gATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTc                                                                                                                   <  1:228462/137‑1 (MQ=255)                        aCGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGGGGGGTTTGATGGGTGGGGGTGTCCACAGTTTGTATATTGttgcggg                                                                                                               >  5:353637/1‑132 (MQ=255)                            gcAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGGCGCTGGGGTTGGGGGGGTGTGTGCACCGGTTCTCTTTTGTTCAGGCGccg                                                                                                           >  7:20853/1‑136 (MQ=255)                                ttGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATg                                                                                                       <  2:222070/137‑1 (MQ=255)                                ttGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATg                                                                                                       <  7:237714/137‑1 (MQ=255)                                ttGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATg                                                                                                       <  3:140586/137‑1 (MQ=255)                                tgggCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAAGCGGCGGCCTGCGGCACCTGGGCCTGGGGGTTCTCGCGAGGCGTGTCGGTTTGCATGGGTGGGGGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATg                                                                                                       <  6:15502/135‑1 (MQ=255)                                 tGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGGTTGGATGGGTGGGTGTGGCCACAGTTTGTTTATTTTTACGGCGCCTTATgg                                                                                                      >  5:242616/1‑137 (MQ=255)                                 tGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGGTTGCCTGGGGGGGGGGGGGCACCGTTTATATATTTTTTAGGGGCCGTAttt                                                                                                      >  2:229958/1‑135 (MQ=255)                                   gCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACGTGGGCCTGCGGGTTCTCTCTAGTCGTTTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGgc                                                                                                    <  8:89978/137‑1 (MQ=255)                                        gggCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGGGGGGTTGGATGGGTGGGTGTGTGCCCAGTTTCTATATTTGTCATGCGGCTTTTGGGCGcccc                                                                                               >  7:294249/1‑136 (MQ=255)                                           cGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTGGGTTTGGATGGGTGGGTGTCTCCACAGTTTCTATATTTTTAAGGCGGCTTATGGGGGccccccc                                                                                            >  5:116084/1‑136 (MQ=255)                                           cGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGGGGGGTTGGATTGGTGGGTGTGTGCCCAGTTTGTTTATTTTTGAGGCGCCAGATGGGGGGCCAccc                                                                                            >  3:89567/1‑136 (MQ=255)                                           cGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGGCGGGTTGCATGGGGGGGGGTGTCCCCAGGTTGTATATTGTTGAGGCGCCTTATGGGGGCCCCCCg                                                                                            >  5:77139/1‑137 (MQ=255)                                             gTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGGATGGGTGGGTGTGGCCACAGGTTGTATATTGTTAAGGGGGCGTTTGGGGGCCCCCCggt                                                                                          >  4:318509/1‑135 (MQ=255)                                                     cAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCAc                                                                                  <  2:86866/137‑1 (MQ=255)                                                     cAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTACATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCAc                                                                                  <  8:322941/137‑1 (MQ=255)                                                       gATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGTGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACtt                                                                                <  7:171833/137‑1 (MQ=255)                                                                 ggAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTGGGTTTGCATGGGTGGGTGTGTCCACAGTTTCTATATTTTTCAGGCGCCGTATGGGCGCCCACCGGTCCGTGCACTTGCTCGATaaa                                                                      >  8:92841/1‑136 (MQ=255)                                                                  gAATCTGCGGCCTGCGGCACCTGGGCCTGCGGGTTCGCGCGAGTCGTGTCGGTTTGCATGGGTGGGAGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAAcc                                                                     <  8:184351/137‑1 (MQ=255)                                                                  gAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAAcc                                                                     <  6:307404/137‑1 (MQ=255)                                                                  gAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAAcc                                                                     <  7:55472/137‑1 (MQ=255)                                                                  gAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAAcc                                                                     <  4:144172/137‑1 (MQ=255)                                                                            ccTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGAt                                                           <  7:96850/137‑1 (MQ=255)                                                                            ccTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGAt                                                           <  3:335334/137‑1 (MQ=255)                                                                                    agcTGGGCCTGCGGGTTCTCGCGAGGCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCGTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAatg                                                   <  7:172743/135‑1 (MQ=255)                                                                                    aCCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAatg                                                   <  2:311390/137‑1 (MQ=255)                                                                                    aCCTGGGCCTGCGGGTTCTCGCGAGTCGTGGCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAatg                                                   <  7:172747/137‑1 (MQ=255)                                                                                        gggCCTGCGGGTTCTCGCGAGTCGTGGCGGTTTGCATGGGTGGGTGTCTCCACAGTTTGTATATTTTTAAGGCGCCTTATTGGGGCCCCCCGTTCCGTCCCATTTGTCGATAAACAAGCCGGGATGCGCAatgcata                                               >  2:169972/1‑136 (MQ=255)                                                                                                   ttCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGGGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATccgccc                                    <  4:67343/137‑1 (MQ=255)                                                                                                   ttCTCGCGAGTCGTGGCGGTTTGCATGGGTGGGTGGCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATccgccc                                    <  8:287208/137‑1 (MQ=255)                                                                                                     ctcGCGAGTCGTGTCGGTTTGCATGGGTGGGTGGCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATccgcccgc                                  <  7:348901/137‑1 (MQ=255)                                                                                                             gcGTGGCGGTTTGCCGGGGTGGGTGTCCCCACAGTTTCTATATTGTTCAGGCGCCTTCTGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATCCGCCCGCGCGGGCGt                          <  4:234559/136‑1 (MQ=255)                                                                                                              cGTGTCGGTTTGGATGGGTGGGTGTGTCCACAGTTTGTATATTGTTAAGGCGCCTTATGGGCGCCCCCCCTTCCGGCCACTTTCTCGATAAACACCCGGGGATTCGCAAATCATGCGCATCCCCCCCCCCGGGCgga                         >  2:19078/1‑135 (MQ=255)                                                                                                                           aTGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATCCGCCCGCGCGGGCGTACCGACTTCGGGAc            <  4:221382/137‑1 (MQ=255)                                                                                                                             gggtgggtGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATCCGCCCGCGCGGGCGTACCGACTTCGGGACAg          <  6:116084/137‑1 (MQ=255)                                                                                                                             ggggggggggCTCCACAGTTTCTATATTGTGCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATCCGCCCGCGCGGGCGTACCGACTTCGGGACAg          <  1:315356/137‑1 (MQ=255)                                                                                                                                  ggtgTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATCCGCCCGCGCGGGCGTACCGACATCGGGACAGACTCa     >  8:343695/1‑137 (MQ=255)                                                                                                                                     ggctcCACTGTTTCTATATTGTGCTGCCGCCTTAGGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACGTCGCGGGGATGCGCAATGCATGCGCATCCGCCCGCGCGGGCGTACCGACTTCGGGACAGACTCAGGa  <  1:313916/135‑1 (MQ=255)                                                                                                                                       |                                                                                                                                       CGACAGTGCCGTTACGCTTGATCACGCGCAGTTGGCCGGGGGCGGTGGCAGCCAGATCCTGGTTGGAATCGGCGGCCTGCGGCACCTGGGCCTGCGGGTTCTCGCGAGTCGTGTCGGTTTGCATGGGTGGGTGTCTCCACAGTTTCTATATTGTTCAGGCGCCTTATGGGCGCCCACCGTTCCGTCCACTTGCTCGATAACCTCGCGGGGATGCGCAATGCATGCGCATCCGCCCGCGCGGGCGTACCGACTTCGGGACAGACTCAGGA  >  KT2440/1348306‑1348574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑