Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,006,012	0	C	T	25.0%	105.1 / 13.9	52	intergenic (‑226/‑250)	ygeV/ygeW	putative sigma(54)‑dependent transcriptional regulator YgeV/putative carbamoyltransferase YgeW
Reads supporting (aligned to +/- strand):  ref base C (15/24);  new base T (13/0);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 6.29e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGGCTTTGATAAAAACATAAGATTTTTATCATTTTCTAATGAAATTATGGAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGAT  >  NC_000913/3005873‑3006150                                                                                                                                            |                                                                                                                                           tGGCTTTGATAAAAACATAAGATTTTTATCATTTTCTAATGAAATTATGGAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTc                                                                                                                                            <  1:1261581/140‑1 (MQ=255) tGGCTTTGATAAAAACATAAGATTTTTATCATTTTCTAATGAAATTATGGAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTc                                                                                                                                            <  1:857402/140‑1 (MQ=255)            aaaaCATAAGATTTTTATCATTTTCTAATGAAATTATGGAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTagc                                                                                                                                 <  2:1382525/140‑1 (MQ=255)                       tttttATCATTTTCTAATGAAATTATGGAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCaaataaat                                                                                                                      <  2:700686/140‑1 (MQ=255)                          ttATCATTTTCTAATGAAATTATGGAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAAATGAAGAGAGATAACCTGCCCCCTTATCTTATTTCTGATACTTAGCAGCAAataaataaa                                                                                                                   >  1:130708/1‑139 (MQ=255)                                               aTGGAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGGTTTTCAAAATGAAGAGAGATAGACCGCCCCCTTATCTTTTTTTTGATATTTAACAGCAAAAAAAAAAAGCGATAAAAAAAACCAAAAGt                                                                                              >  2:295623/1‑140 (MQ=255)                                                 ggAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGttt                                                                                            <  2:1163547/140‑1 (MQ=255)                                                     gagaTATCACATTTCTATATCAATATGAGAATTACGGCGGTGGGGTTTTTAAAATGAAGAGAGATAACCTGCCCCCTTTTCTTATTTTTGATAATTTGCAGCAAAAAAAAAAAGCGATAAAAAAAACCAAAAGtttttct                                                                                        >  2:244526/1‑137 (MQ=255)                                                     gagaTATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATTAAACTGAAGAGAGATAGCCTGCCCCTTTTTCTTTTTTTTGATACTTTGCAGCAAATAAATAAAGCGATAAAAAAAACCAAAAGATTTTGt                                                                                        >  1:1189834/1‑140 (MQ=255)                                                     gagaTATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGt                                                                                        <  1:244526/140‑1 (MQ=255)                                                      agaTATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGGTTATCAAAATGAAGAGAGATAACCTGCCCCTTTATCTTATTTTTGATACTTAGCAGCAAATAAAAAACACGATAAAAAAAAACAAACGTTTTTGtt                                                                                       >  2:462264/1‑139 (MQ=255)                                                         gagacagtttCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTAttt                                                                                    <  2:838116/133‑1 (MQ=255)                                                          atCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAAATGAAGAGAGATAGCCTGCCCCCTTATCTTATTTTTTATACTTTGCAGCAAAAAAAAAAAGCGATAAAAAAAACCAAAAGTTTTTGTAtttt                                                                                   >  1:545125/1‑140 (MQ=255)                                                              caTTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTacaa                                                                               <  2:801630/140‑1 (MQ=255)                                                               aTTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTacaaa                                                                              <  1:295623/140‑1 (MQ=255)                                                                tttCTATATCAATATGAGAATTACGGCGGTGAGGTTATCAAACTGAAGAGAGATAGCCTGCCCCCTTATCTTTTTTTTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAACCAAACGTTTTCGTATTTTacaaaa                                                                             >  1:798012/1‑139 (MQ=255)                                                                 ttCTATATCAATATGAGAATTACGGCGGTGAGTTTATTAAAATGAAGAGAGATAGCCTGCCCCTTTATCTTTTTTTTTATACTTAGCAGCAAATAAATAACGCGATAAAAAAAACCAAACGTTTTTGTATTTTtcaaaaa                                                                            >  1:90000/1‑138 (MQ=255)                                                                  tCTATATCAATATGAGAATTACGGCGGTGAGGTTTTCAAACTGAAGAGAGATAACCTGCCCCTTTATCTTATTTTTTATACTTAGCAGCAAAAAAAAAAAGCGATAAAAAAAACCAAACGGTTTTGTATTTTtaaaacaa                                                                           >  2:654906/1‑140 (MQ=255)                                                                   cTATATCAATATGAGAATTACGGCGGTGAGGTTATCAAAATGAAGAGAGATAGCCTGCCCCCTTTTCTTATTTTTGATACTTAGCAGCAAATAAAAAACGCGATAAAAAAAACCAAAAGTTTTCGTATTTTTCAaaaaac                                                                          >  1:1236855/1‑140 (MQ=255)                                                                     atatCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCa                                                                        <  2:607846/140‑1 (MQ=255)                                                                       atCAATATGAGAATTACGGCGGTGAGGTTATCAAACTGAAGAGAGATAACCTGCCCCCTTATTTTTTTTTTGATACTTAGCAGCAAAAAAAAAACGCGATAAAAAAAAACAAACGTTTTCGTATTTTACAAACAACCAGa                                                                      >  2:225461/1‑140 (MQ=255)                                                                         cAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAg                                                                    <  1:462264/140‑1 (MQ=255)                                                                           atatGAGAATTACGGCGGTGAGTTTTTCAAAATGAAGAGAGATAACCTGCCCCTTTATTTTTTTTTTGATACTTTGCAGCAAATAAAAAAAGCGATAAAAAAAACCAAACGTTTTCGTATTTTTCAAACAAccccgtctc                                                                  >  1:838116/1‑133 (MQ=255)                                                                           atatGAGAATTACGGCGGTGAGGTTATTAAAATGAAGAGAGAAAACCTGCCCCTTTTTTTTATTTTTGATAATTAGCAGCAAAAAAAAAAAGCGATAAAAAAAAACAAAAGTTTTTGTATTTTTCAAAAAAACAGAAACt                                                                  >  2:23010/1‑140 (MQ=255)                                                                            tatGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCCTTATCTTATTTCTGATACTTAGCAGCAAAAAAATAAAGCGATAAAAAAAACCAAACGTTTTTGTATTTTACAAACAACCAGAAGCTg                                                                 >  1:807066/1‑140 (MQ=255)                                                                            tatGAGAATTACGGCGGTGAGGTTTTCAAACTGAAGAGAGAAAGCCTGCCCCCTTTTCTTTTTTTTTTTACTTAGCAGCAAATAAAAAACGCGATAAAAAAAACCCAACGTTTTTTTATTTTTCAAACAACCAAAAACTg                                                                 >  2:763833/1‑140 (MQ=255)                                                                                agaATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCAt                                                             <  1:876668/140‑1 (MQ=255)                                                                                agaATTACGGCGGTGAGGTTTTCAAACTGAAGAGAGATAGCCTGCCCCTTTTTCTTTTTTTTGATACTTAGCAGCAAAAAAAAAAAGCGATAAAAAAAACCAAACGTTTTTGTATTTTTCAAACAAACAGAAGCTGGCAt                                                             >  2:852710/1‑140 (MQ=255)                                                                                 gaATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATc                                                            <  2:153161/140‑1 (MQ=255)                                                                                 gaATTACGGCGGTGAGTTTATCAAAATGAAGAGAGAAAGCCTGCCCCTTTTTCTTTTTTTTTTTACTTAGCAGCAAAAAAAAAAAACGATAAAAAAAACCAAACGGTTTTGTATTTTTCAAAAAAACAAAAACGGGCATc                                                            >  2:1386060/1‑140 (MQ=255)                                                                                   aTTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTTTGATACTTAGCAGCAAATAAAAAACGCGATAAAAAAAACCAAACGTTTTTGTATTTTACAAACAACCAGAAGCTGGCATCaa                                                          >  1:93101/1‑140 (MQ=255)                                                                                   aTTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCCTTATCTTATTTTTGATACTTAGCAGCAAATAAATAAAGCGATAAAAAAAACCAAACGTTTTTGTATTTTTCAAAAAAACAGAAACTGGCATCaa                                                          >  1:781912/1‑140 (MQ=255)                                                                                   aTTACGGCGGCGAGTTTATCAAAATAAAGAGAGAAAGCCTGCCCCTTTATCTTTTTTCTCATAATTAGCAGCAAATAAAAAAAGCGCTAAAAAAAGCCAAAAGATTTTGTATTTTACAAACAACCAGAAGCTGGcaacaa                                                          >  2:1171288/1‑140 (MQ=255)                                                                                       cggcggTGAGGTTTTTAAAATGAAGAGAGATAGCCTGCCCCCTTTTCTTTTTTTTGATAATTAGCAGCAAAAAAAAAAAGCGATAAAAAAAACCAAACGTTTTTGTATTTTTCAAACAAACAGAAACTGGCATCAAtttt                                                      >  2:932530/1‑139 (MQ=255)                                                                                           ggTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGAt                                                  <  1:1171288/140‑1 (MQ=255)                                                                                           ggTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGAt                                                  <  1:670513/140‑1 (MQ=255)                                                                                           ggTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGAt                                                  <  1:852710/140‑1 (MQ=255)                                                                                             tGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCa                                                <  2:1189834/140‑1 (MQ=255)                                                                                             tGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCa                                                <  2:545125/140‑1 (MQ=255)                                                                                                 tttATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAAccc                                            <  2:130708/140‑1 (MQ=255)                                                                                                 tttATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAAccc                                            <  2:90000/140‑1 (MQ=255)                                                                                                 tttATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAAccc                                            <  1:352736/140‑1 (MQ=255)                                                                                                         aCTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACAtt                                    >  1:1197954/1‑140 (MQ=255)                                                                                                               gagagaTAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGt                              <  1:932530/140‑1 (MQ=255)                                                                                                                   gaTAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCaaa                          >  1:216227/1‑140 (MQ=255)                                                                                                                    aTAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAAt                         >  1:1388324/1‑140 (MQ=255)                                                                                                                    aTAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAAt                         >  2:1248368/1‑140 (MQ=255)                                                                                                                       gCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAg                      >  2:44464/1‑140 (MQ=255)                                                                                                                       gCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAg                      >  1:168671/1‑140 (MQ=255)                                                                                                                            ccccTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCttt                 >  2:461311/1‑140 (MQ=255)                                                                                                                            ccccTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCttt                 >  2:587799/1‑140 (MQ=255)                                                                                                                                 ttATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAg            <  1:587799/140‑1 (MQ=255)                                                                                                                                  tATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGc           >  2:1230192/1‑140 (MQ=255)                                                                                                                                  tATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGc           >  1:251795/1‑140 (MQ=255)                                                                                                                                      ttATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCcgcg       <  2:798012/140‑1 (MQ=255)                                                                                                                                       tATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCcgcgc      >  2:753598/1‑140 (MQ=255)                                                                                                                                         tttCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCgg    >  2:582898/1‑140 (MQ=255)                                                                                                                                           tCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGTAGCCGCGCGGAt  >  1:1361229/1‑140 (MQ=255)                                                                                                                                           tCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGAt  <  1:763833/140‑1 (MQ=255)                                                                                                                                           tCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGAt  <  1:654906/140‑1 (MQ=255)                                                                                                                                            |                                                                                                                                           TGGCTTTGATAAAAACATAAGATTTTTATCATTTTCTAATGAAATTATGGAAGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGAT  >  NC_000913/3005873‑3006150

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑