Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	3,725,209	+T	intergenic (‑41/‑488)	U712_19205 ← / → U712_19210	Uncharacterized protein ywcI/Minor extracellular protease vpr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	3,725,205	1	.	T	80.0%	114.0 / 25.9	48	intergenic (‑37/‑492)	U712_19205/U712_19210	Uncharacterized protein ywcI/Minor extracellular protease vpr
Reads supporting (aligned to +/- strand):  ref base . (2/7);  new base T (30/6);  total (35/13)
Fisher's exact test for biased strand distribution p-value = 1.01e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑C‑TTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGT  >  CP006881/3725069‑3725329                                                                                                                                            |                                                                                                                                gAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑C‑tg                                                                                                                               >  7:255088/1‑138 (MQ=255)       aaTAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑C‑ttt‑ttagc                                                                                                                        >  1:139459/1‑135 (MQ=255)          aGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACAATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTGGTTTTGGCCGGCC‑GC‑CGTTT‑T‑a‑gc                                                                                                                       >  5:43423/1‑136 (MQ=255)            accgCGGCAGCCGCAGGTTTTCTGTCCGGCGTCACCCAGGTACTCAAAAAGACCCTCCACACCCGGAAAGATGCAAGCACACGATGAATAGCTCAACATCCCTCCGCGTCATTTTTGAAGGCAGGC‑T‑TTT‑T‑A‑GAAGccc                                                                                                                  >  7:168510/4‑139 (MQ=255)              cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGt                                                                                                                >  1:283620/2‑139 (MQ=255)               gCGGCAGCCGGAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAACCATCACGCCGCTGCTTGTTGGGAGGCC‑GG‑C‑TTTGT‑A‑GCAGccc                                                                                                                  >  6:330786/1‑136 (MQ=255)                 ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCC‑GC‑CGTTT‑T‑A‑GCAGCCCGttt                                                                                                              >  7:119151/1‑138 (MQ=255)                 ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGt                                                                                                                >  5:115106/1‑136 (MQ=255)                 ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGATTCATAG‑AAAACATCCCTCCGCTACTTTTTGGAAGGCC‑GC‑CTTTT‑T‑A‑GCAGCCCGGTTtc                                                                                                            >  8:265480/1‑139 (MQ=255)                    aGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCCGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGgttt                                                                                                             >  3:277012/1‑136 (MQ=255)                    aGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGttt                                                                                                              >  3:365273/1‑135 (MQ=255)                    aGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CGTTT‑T‑A‑GCAGCCCGttt                                                                                                              >  4:201096/1‑135 (MQ=255)                                                   ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCATCCGCAGCCCGCAAGAAAAGACGGCCGAtt                                                                           >  8:239090/1‑139 (MQ=255)                                                      atcaAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtt                                                                           >  5:214303/1‑136 (MQ=255)                                                        caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAgttcttt                                                                      >  7:265628/1‑139 (MQ=255)                                                        caAAAAGACCATCCACACCCGAAAAGATACAACCAAACGTTGCATAGAAAAACATCCCTCCGCTTCTTTTTGGCCGGCA‑GC‑CTTTT‑T‑A‑GCCGCCCGTTTTCTCCGCCCCACCCCGCAAGAAAACACGGCCGAtttc                                                                         <  4:185941/136‑1 (MQ=255)                                                           aaaGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtttgttttct                                                                   >  1:129917/1‑139 (MQ=255)                                                           aaaGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtttcttt                                                                      >  5:145792/1‑136 (MQ=255)                                                                ccATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGGTTTCTCAGCCGCATCCCGCAAGAAAAGACGTCCGAtttgttttggagca                                                               >  8:384754/1‑132 (MQ=255)                                                                   tCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCa                                                               >  5:308901/1‑135 (MQ=255)                                                                         cccGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGc                                                     >  8:317759/1‑139 (MQ=255)                                                                           accacggATATATGCAAAGGTTTATTATAAAAAATACCCTGCGTTTTTTTTTGGCCGGCAGGA‑T‑TTT‑T‑A‑GCTGCCCGTTTTCTCTCCCGCTCCGCGCATCAAACCTCGGCCGATTTCTTTTCTCGCAAACTAGCGGctc                                                   <  8:326442/133‑1 (MQ=255)                                                                             tAAAGATACAAGCAAACGTTTCATAGAAAACCATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGTCCGATGTCGTTTCTCGCAAACTAGCCGcgc                                                   >  7:27174/1‑135 (MQ=255)                                                                                aGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc                                                   >  3:178612/1‑134 (MQ=255)                                                                                  aTACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAg                                                >  5:413402/1‑135 (MQ=255)                                                                                    aCAACCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGTCAGGCA‑GC‑CTTTT‑T‑T‑GCAGCCCGTTTTCACAGCCGCAGCCCCCAAGAAAAGACGGCCGAATTATTTTCTCGGAAACTAGCGGCTCATGCaaaa                                           >  7:9713/1‑138 (MQ=255)                                                                                     cAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCat                                             >  4:116548/1‑134 (MQ=255)                                                                                       aGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTATCGCAAACTAGCGGCTATAGCAAAAc                                          >  4:211782/1‑136 (MQ=255)                                                                                        gCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                      <  7:317759/139‑1 (MQ=255)                                                                                        ccAAACGTTTCAAACAAAAACATCCCCCCGCTTCTTTTGGGCAGGCC‑GC‑CTTTT‑T‑C‑GCCGCCCGTTTTCTCCCCCCCCCCCCGAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                      <  2:283620/138‑1 (MQ=255)                                                                                          acaCGTTGAATACAAAAACAGCCCCCCGCTTTTTTTGGGCCGGCA‑GCTT‑TTT‑T‑C‑GCCGCCGGTTTTCGCCGCCGCCGCCCCCACCAAACCACGGCCGATTTCTTTTCTCGAAAACTAGCGGCTCTAGCAAAACTCa                                       <  6:308901/134‑1 (MQ=255)                                                                                          aaaCTTTTCATAAAAAAACAGCCCTCCGCTTCTTTTTGGCAGGCC‑GCGT‑TTT‑T‑A‑GCCGCCCGTTTACTCAGCCGCAGCCCGAAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCa                                       <  3:211782/136‑1 (MQ=255)                                                                                          aaaCGTTTCATACAAAACCATCCATCCGGTGATTTTTGGCCCGCA‑GC‑CTTTT‑T‑C‑GCAGCCGTTTTTCTCAGCCGCCCCCCGCAACAAACCACGGCCGTTTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCa                                       <  6:413402/136‑1 (MQ=255)                                                                                            ccttttAATATAAAAACATCCCTCCGTTTGTTTTTGGCTGGCA‑GC‑T‑TTT‑TAA‑GCTCCCGTTTTTCTCAGCCGCCGCCCCAATTAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATg                                     <  6:214303/133‑1 (MQ=255)                                                                                            ccGTTTAATAGAACAACACCCCTCCGGTTCTTTTGGCCAGGCA‑GC‑C‑TTT‑T‑ACCCTCCCCTTTTTCTCCGCCGCCGCCCCAAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAACCTCATGAct                                  <  8:119151/138‑1 (MQ=255)                                                                                            aggTTTAATACAAAAACATCCCTCGGCTTATTTTGGGCAGGCA‑GCTT‑TTT‑T‑C‑GCTGCCCGTTTTCTCAGCCGCAGCCCGCATGAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                  <  7:239090/137‑1 (MQ=255)                                                                                            aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTGTCGCAAACAAGCGGCTCTAGCAAAACTccagtc                                   >  7:326442/1‑133 (MQ=255)                                                                                            aCGTTTAATAGAAAAACACCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑C‑GCAGCCCGTTTTCTCCCCCGCAGCCCCCAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                  <  7:229833/139‑1 (MQ=255)                                                                                            aCGTTACATACAAAACCCTCCCTCCGCTTCTTTTTGGCAGCCC‑GCAT‑TTT‑T‑C‑GCCCCCCTTTTCCTCCGCCGCCCCCCGAAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                  <  2:139459/139‑1 (MQ=255)                                                                                               tttCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                  >  3:216040/1‑136 (MQ=255)                                                                                               tttCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTATTTTATCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                  >  4:169773/1‑136 (MQ=255)                                                                                               tttCATAGAAAAACATCCCTCCGCTTCTTTTTGGCACGCC‑GC‑CTTTT‑T‑A‑TCAGCCCGTTTTCTCAGCCGCAGCCCTCAACAAAAGACGGAGGAATTCTTTTATCGAAATCTGTCCGCTCGAGCAAAAATCATGCct                                  >  6:51714/1‑136 (MQ=255)                                                                                                 tCATAGAAAAACATCCCTCCGCTTCTTTTTGGCCGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCCAACTAGCGGCTCGAGCAAAACTGATGACGCTATg                             >  2:54646/1‑139 (MQ=255)                                                                                                    tAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCGTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAcgagat                              >  6:315501/1‑130 (MQ=255)                                                                                                       aaaaaCATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGAGTTCGTTTGTCGCACACTAGCGGCTGTAGCAAAACTCATGGCTGTTTGTTAGAc                       >  2:301827/1‑139 (MQ=255)                                                                                                          aaCATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGAc                       >  6:303633/1‑136 (MQ=255)                                                                                                               cccTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTATTTTCTCGCCAACTAGCGGGACTAGGAAAACTCATGACTCAATGATAGCCCGTGGaaa               >  8:223844/1‑139 (MQ=255)                                                                                                                         cttTTTGGCAGGCA‑GC‑CTTTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATTGACCGTGGAAAGAGaaa         >  3:388116/1‑134 (MQ=255)                                                                                                                            tttGGCAGGCA‑GC‑CTTTT‑T‑A‑GAAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGGTCTAGCAAAACTCAAGACTCTATGATATAACCTGGAAAGAGAATTCCTTGt  >  8:192367/1‑139 (MQ=255)                                                                                                                             ttGGCAGGCT‑GC‑CTTTT‑T‑A‑GCACCCCGTTTTCTCTGCCGCAGCCCCAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCtt     <  4:388116/135‑1 (MQ=255)                                                                                                                                            |                                                                                                                                GAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑C‑TTT‑T‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGT  >  CP006881/3725069‑3725329

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: ‑