Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	ACB143	4,624,111	C→A	14.9%	intergenic (+117/+181)	CJ019_04367 → / ← pgsA	hypothetical protein/CDP‑diacylglycerol‑‑glycerol‑3‑phosphate 3‑phosphatidyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB143	4,624,111	0	C	A	14.9%	104.0 / 2.3	54	intergenic (+117/+181)	CJ019_04367/pgsA	hypothetical protein/CDP‑diacylglycerol‑‑glycerol‑3‑phosphate 3‑phosphatidyltransferase
Reads supporting (aligned to +/- strand):  ref base C (26/19);  new base A (2/7);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 7.21e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTCCAGGTAGCCCACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTCCCGCGTCGTG  >  ACB143/4623984‑4624234                                                                                                                                  |                                                                                                                            tGTCCAGGTAGCCCACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGAAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACtt                                                                                                                     <  2:11529/136‑1 (MQ=255)      cggTAGCCAACGGCGTCACTGCCAGGGCGCCGCGTTGTGGTTTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGa                                                                                                                <  8:23500/135‑1 (MQ=255)      aGGTAGCCCACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGa                                                                                                                <  1:305848/136‑1 (MQ=255)         tAGCCCACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACtt                                                                                                             >  6:57452/1‑136 (MQ=255)         tAGCCCACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACtt                                                                                                             >  2:34911/1‑136 (MQ=255)         tAGCCCACGGCGTCACGGCCAGGGCGCCGCGGTGTGGTGTTTGTACTTGAATTTCGGAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCACGAAGGGC‑CTGTTTTCAACGACTTACAGACtt                                                                                                             >  5:358900/1‑136 (MQ=255)           gCCCACGGCGTCACGGCCAGGGCGCCGGGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCg                                                                                                           <  4:342708/136‑1 (MQ=255)           gCCCACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTc                                                                                                            >  1:223895/1‑135 (MQ=255)           gCCCACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTc                                                                                                            >  8:206047/1‑135 (MQ=255)              cACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAATGGC‑CTTTTTTAAACGACTTACATCCTTCGAcg                                                                                                        >  7:173195/1‑135 (MQ=255)               aCGGCGTCACGGCCAGGGCGCCGCGTTGGGGTGTTTTTACTTGAATTTCGTTGAGGGCGGGGTATTGAGGCAGCATGC‑ATTCGAAAGAAAAAAGTCCCCGAAGGGC‑CTTTTTTCAAAGACTTAAACACTTCGACt                                                                                                        >  7:87701/1‑135 (MQ=255)                cGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGAc                                                                                                         <  4:360987/133‑1 (MQ=255)                cGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGAc                                                                                                         >  3:360987/1‑133 (MQ=255)                cGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTg                                                                                                       >  5:181200/1‑135 (MQ=255)                cGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTg                                                                                                       >  4:228913/1‑135 (MQ=255)                cGGCGTCACGGCCAGGGCGCCGCGTGGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTg                                                                                                       >  5:160602/1‑135 (MQ=255)                   cGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTTCTTGAATTTCGTAGAGGGCGGGGTTTTGAGGCAGTATGG‑ATTGGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTAAACGACTTAAATACATAGACTGCAAc                                                                                                   >  6:37444/1‑136 (MQ=255)                         ggCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTg                                                                                                >  4:71675/1‑133 (MQ=255)                                gcgcCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTa                                                                                      >  7:58017/1‑136 (MQ=255)                                  gcggcgTTGTGGTGTTTGTACTTGATTTTCGTTGAGGGCGGGGTATTGAGGCATAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTAtt                                                                                    <  6:209087/133‑1 (MQ=255)                                              tgtTTTTATTTTAATTTCGTTGAGGGGGGGTTATTTTGGAATAATGA‑ATTGTAACGAAAAAAGGCCCCTAAGGGC‑ATTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGaa                                                                         <  1:379690/135‑1 (MQ=255)                                                 ttGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAAc                                                                       >  6:137187/1‑134 (MQ=255)                                                   gTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACATGTAGAACTTAATTTGGAGCGGGAAACgag                                                                    >  6:358015/1‑135 (MQ=255)                                                     aCTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACt                                                                 >  2:95108/1‑136 (MQ=255)                                                           aTTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACTAAAAAAGGCCCCTAAGGGC‑ATTTTTTAAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGTAGCGGGAAACGAGACTCGAAc                                                            <  7:318984/135‑1 (MQ=255)                                                             ttCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTcg                                                         >  1:161873/1‑136 (MQ=255)                                                                 tAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGAc                                                     >  3:385581/1‑136 (MQ=255)                                                                         ggggTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCt                                             >  6:28589/1‑136 (MQ=255)                                                                          gggTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCtt                                            <  2:223895/136‑1 (MQ=255)                                                                           ggTTTTGAGGCATAATGC‑ATTCTAACTAAAAACGGCCCCGACGGGC‑CTTTTTTCAACTACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAACCGAGACTCGAACTCGCGACCCCGACCTTg                                           <  2:101573/136‑1 (MQ=37)                                                                           ggTATTGCGGCAGAATCC‑ATTCAAAGCAAAAACGCCCCCCAGGGGC‑ATTTTTTCAACGACTTCCAGACTTCGACTGAAACGTGTCTATCTTTATTTGGCGCGGGAAACGAGACTCGAACCCGCGACCCCGACCTTg                                           <  4:252791/136‑1 (MQ=21)                                                                           ggTATTGAGCCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAACCCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTg                                           <  2:241216/136‑1 (MQ=255)                                                                            gTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTgg                                          >  7:204286/1‑136 (MQ=255)                                                                                   ggCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGt                                                                                               >  3:112317/1‑76 (MQ=255)                                                                                   ggCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGt                                                                                               <  4:112317/76‑1 (MQ=255)                                                                                   ggCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTc                                   >  1:201245/1‑136 (MQ=255)                                                                                    cgatattGC‑ATGCGAACCAAAAACGG‑CCCGCAGGGCGGTTTTTTCAAGGTCTTACAGACTTCCACTGAACCGTGTATAACTTTTTTTGGAGCGGGAAACTCGCGTCGAACGCGCGACCCCGACCTTGGCAAGGTCg                                  <  2:45813/130‑1 (MQ=12)                                                                                     caaaaTGCAATTCTAACAAAAACCGCCCCCTATGGGC‑TTTTTTAAAACGACTAACACACTTCGACTCAACCCTGTAGATCTTTATTTGGCGCGGCAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCg                                  <  8:133667/133‑1 (MQ=12)                                                                                       taaTGC‑ATTCTAACTAAAAAAGCCCCCGAAGGGC‑ATTTTTTAAACGACTTACAGACTTCGACTGAAACCTGTATATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGc                               <  6:58393/135‑1 (MQ=25)                                                                                       gAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGc                               <  7:206047/136‑1 (MQ=255)                                                                                          tGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGctc                             >  8:219993/1‑135 (MQ=255)                                                                                                  gaacgaaAACCGGCCCCGAAGGGC‑CTTTTTTAAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACt                     <  5:299627/136‑1 (MQ=255)                                                                                                      gaaAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGc                 >  4:22860/1‑136 (MQ=255)                                                                                                         aaacGGCCCCCAAGGGC‑CTTTTTTAAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTAt              <  6:140527/136‑1 (MQ=255)                                                                                                          aacggCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTAtt             <  6:353942/133‑1 (MQ=255)                                                                                                          aacgcccccGACGGGC‑CTTTTTTCAACGACTAACAGACTTCAACTGAACCCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTAtt             <  5:88011/131‑1 (MQ=18)                                                                                                            aGGCCCCTAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTCAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTcc           <  6:58996/136‑1 (MQ=255)                                                                                                                  cGAAGGGC‑CTTTTTTCAACGACTTACAGAGTTGGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTCCCGcgtc     <  7:27600/136‑1 (MQ=255)                                                                                                                    aaGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTCCCGcgtcgt   >  3:79225/1‑136 (MQ=255)                                                                                                                     aGGGC‑TTTTTTTAAACGACTTACAGACTTCTACTTAAACCTGTAGATCTTTATTTGGCGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTCCCGcgtcg    <  5:276785/134‑1 (MQ=18)                                                                                                                     aGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTCCCGCGTCGTg  >  4:398571/1‑136 (MQ=255)                                                                                                                      tgggattttttaAAACGAATTACACACTTCGACTGAAACCTTTATATATTTATTTGGCGCGGCAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTCCCGcgtcgt   <  2:201245/129‑1 (MQ=17)                                                                                                                              ttttCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGa                                                      >  4:233383/1‑76 (MQ=255)                                                                                                                              ttttCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGa                                                      <  3:233383/76‑1 (MQ=255)                                                                                                                                  |                                                                                                                            TGTCCAGGTAGCCCACGGCGTCACGGCCAGGGCGCCGCGTTGTGGTGTTTGTACTTGAATTTCGTAGAGGGCGGGGTATTGAGGCAGAATGC‑ATTCGAACGAAAAAAGGCCCCGAAGGGC‑CTTTTTTCAACGACTTACAGACTTCGACTGAAACCTGTAGATCTTTATTTGGAGCGGGAAACGAGACTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTCCCGCGTCGTG  >  ACB143/4623984‑4624234

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: ‑