Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,958,771	0	A	T	44.2%	69.2 / 30.3	52	D38E (GAT→GAA)	ptrA	protease III
Reads supporting (aligned to +/- strand):  ref base A (3/26);  new base T (23/0);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.47e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTAATTTTCTGTC  >  NC_000913/2958631‑2958917                                                                                                                                              |                                                                                                                                                          cccTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑c                                                                                                                                               <  1:786536/151‑1 (MQ=255)              cGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTTTCTTTTTTA‑CTTTTT‑CGGGTGGGTTTCt                                                                                                                                   >  1:578187/1‑150 (MQ=255)                 gATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGGATTTTTTTTTTAA‑Ctttttggatgggtt                                                                                                                                        >  2:508784/1‑134 (MQ=255)                 gATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTCACCTTTTA‑TGGTGGGTTTcttaa                                                                                                                                 >  2:304242/1‑146 (MQ=255)                       ccAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTTTCTTTTTCT‑CCTTTT‑TCGATGGGTTTCTG‑TATctcct                                                                                                                         >  1:248887/1‑146 (MQ=255)                                  aCGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGttt                                                                                                            <  2:42838/151‑1 (MQ=255)                                    gggCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCt                                                                                                          <  1:792928/151‑1 (MQ=255)                                       cacctcCAGCGCCGAGAGCGATTTAACTGCCTTCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGc                                                                                                        <  1:545615/150‑1 (MQ=255)                                        accaccAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTTTTTTTTTTT‑CTTTTT‑TGGATGGTTTTCTT‑TAATGGCTG‑GCCTCCCGCTTCt                                                                                                          >  1:680162/1‑147 (MQ=255)                                             caGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑tt                                                                                                <  1:654752/151‑1 (MQ=255)                                              aGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTA‑CTTTTA‑CGGGTGGGTTTCTT‑AATCGGCTG‑CCCTCCCCGTTTTTCCTGAC‑tt                                                                                                >  1:154800/1‑150 (MQ=255)                                               gcgcCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑aa                                                                                             <  2:287410/151‑1 (MQ=255)                                                 gcCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTTTCTTTTTCA‑CTTTTT‑CGGGTGGGTTTCTG‑GATTCGCTG‑TCCTCCCCCTTCTTCCTGCC‑ttta                                                                                              >  1:575130/1‑147 (MQ=255)                                                   cGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTTTTA‑CTTTTT‑TGGATGGGTTTCTT‑AATTGGGTG‑CCATCCCCCTTTTTCCTTAC‑TT‑TA‑ggg                                                                                         >  1:59574/1‑150 (MQ=255)                                                   cGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGt                                                                                        <  1:873147/151‑1 (MQ=255)                                                    gagaGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTA‑CTTTTT‑CCGGTGGGTTTCTG‑AAACCGCTG‑GCCTCCCCTTTTTTCCTTAC‑TT‑AA‑agggg                                                                                       >  2:11568/1‑149 (MQ=255)                                                      gagCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTTTTT‑CTTTTT‑TGGAAGGGTTTCTG‑AATTGGCTG‑GCATCCCCCTTTTGTCTGTCTTT‑AA‑ggggg                                                                                       >  2:293509/1‑148 (MQ=255)                                                           aTTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTTTCTTTTTCA‑CTTTTA‑CGGATGGGTTTCTG‑TATTCGCTG‑CCCTCCCGTTTCTGCCTGAC‑TT‑AA‑GGGGGcccca                                                                                  >  1:556082/1‑147 (MQ=255)                                                             ttAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAgg                                                                               <  2:246189/150‑1 (MQ=255)                                                             ttAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAgg                                                                               <  2:866471/150‑1 (MQ=255)                                                                   gcctgcGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAAc                                                                          <  1:434896/149‑1 (MQ=255)                                                                   gcctgcGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACt                                                                         <  2:278448/150‑1 (MQ=255)                                                                   gcctgcGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTa                                                                        <  1:898752/151‑1 (MQ=255)                                                                       gcGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTaacaa                                                                    <  2:657208/151‑1 (MQ=255)                                                                            tCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTT‑ATTTTT‑CGGATGGTTTTCTG‑TATCGGCTG‑CCCTCCCGTTTTTTCCTGAC‑TTAAA‑GGGGGCCCAAA‑GGCAACCAAcaaaaa                                                                 >  1:336448/1‑149 (MQ=255)                                                                             cAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACaata                                                               <  2:180236/150‑1 (MQ=255)                                                                              aGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑ATATCTTTTTCT‑CTTTTT‑TCGGTGGGTTTCTG‑AATCTGCCGCCCCCCCCTTTTTTCCCTGCT‑TT‑AA‑GGGGGCCCAAAGGGCacaaacaaaaaaaa                                                               >  2:365521/1‑137 (MQ=255)                                                                               gAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTTTTTTTTTTA‑CTTTTT‑AGGGTGGGTTTCTT‑GATCGGCTG‑CCCCCCCCCTTTTTCCTGACTTT‑AA‑GGGGGCCCAAA‑GGCAACCAACAACaaaaa                                                              >  1:609282/1‑149 (MQ=255)                                                                                 aaCCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTT‑TGGGGGGGTTTCTT‑AATCCGGTG‑GCCTCCCCTTTTTTCCCGAC‑TT‑AA‑GGGGGGCCAAAGGGGAAATAACaaaaaaaa                                                              >  2:58125/1‑147 (MQ=255)                                                                                  aCCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTTTTT‑CTTTTT‑TGGGAGGTTTTTTG‑AATAAGCCG‑GCATCCCCCTTTTGCCTTACTTT‑AG‑GGGGGGCCAAGGGGCAACaaaaaaaaaaaaacct                                                          >  2:563252/1‑147 (MQ=255)                                                                                        aaGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAAcc                                                   <  1:172430/151‑1 (MQ=255)                                                                                          gACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTA‑CTTTTA‑TAGGTGGGTTTCTGAAACCGGGTC‑CCCTCCC‑CTTCTTCCTCAC‑TT‑AA‑GGGGGCCCCAAAGGCGAATAACaaaaaaaaaagtttttacc                                                   >  1:284651/1‑138 (MQ=255)                                                                                            ccaccaTACCGTTATCCAGAAGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAgg                                                <  1:424170/150‑1 (MQ=255)                                                                                              accaTACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTT‑CTTTTT‑AGGGTGGGTTTCTG‑AATCGGGCG‑CCCTCCCGCTTTTTCCTGAC‑CT‑AA‑GGGGGCCCAAAAGGCCACTAAAAACAAAAAAGCTTTTAAACaaggg                                              >  1:34896/1‑146 (MQ=255)                                                                                                 aTACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTA‑CTTTTT‑CTGATGGGTTTCTT‑AAACGGCCG‑CCCTCCCCTTTTTTCCTTACTTT‑AG‑GGGGGCCCAAAGGG‑AACTAAAAAAAAAAAAGCtttttaacacggg                                              >  1:119989/1‑137 (MQ=255)                                                                                                    ccGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCggg                                       <  1:48516/151‑1 (MQ=255)                                                                                                    ccGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCggg                                       <  1:754235/151‑1 (MQ=255)                                                                                                    ccGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGCTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCggg                                       <  1:694056/151‑1 (MQ=255)                                                                                                     cGTTATCCAGACGTATAGCCTGATACTGGCGG‑CTTTCTTTTTTA‑ATTTTACCGAATAGTTCCTTG‑AACAGCACC‑CCCGCCCGTTTTTGCC‑GTT‑TT‑AA‑GGGTGGCCAAAAGACAACTAATCACAAAAAAATTTTGTACCAGGtggggccg                                        >  2:859983/1‑143 (MQ=255)                                                                                                      gTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGc                                     <  2:190692/151‑1 (MQ=255)                                                                                                       ttATCCAGACGTATAGCCTGATACTGGCGG‑TTTTTTTTTTTA‑CTTTTT‑TGGGTGGGTTTCTG‑AAACGGGCG‑CCCTCCCCCTTTTTCCTTTCTTT‑AA‑GGGGGCCCAAAAGGAAACCAA‑AACAAAAATACTTTTTAACAGGGGGCGCgggg                                      >  2:580918/1‑149 (MQ=255)                                                                                                        tATCCAGACGTATAGCCTGATACTGGCGG‑GTATTTTTTTTT‑CTTTTT‑CGGGGGGGTTCCCG‑AATATGGCG‑CCATCCCCTTTTTTCCTTACTTT‑AA‑GGTGGCCCAAAGGG‑AACTAACAACAAAAAAGCTTTTAAACAGGGGGTGCgggg                                      >  2:79438/1‑148 (MQ=255)                                                                                                            cAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCAc                               <  2:556509/151‑1 (MQ=255)                                                                                                              gACGTATAGCCTGATACTGGCGG‑TTATCTTTAGCT‑CTTTTA‑CGGATGGTTTACTG‑AATCGGATT‑CGATCCCGTTTGTGCCTGAC‑GT‑AA‑GGGTGCCCAGAGGGCAACTAACAACAATAATGCTTTGACCCAGGTGCTGCGGGGCATTCAc                               <  2:467865/149‑1 (MQ=255)                                                                                                               aCGTATAGCCTGATACTGGCGG‑TTATTTTTTTTA‑TTTTTT‑TGGATGGGTTTCTG‑AAACTGGTG‑CCCTCCCCTTTCTTCCTGTC‑TT‑AATGGGGGCCCAAAGGG‑AAATAAAAACAAAAAAGCTTTTTAACAGGGGCTGCgggggggtcaacg                             >  2:619955/1‑141 (MQ=255)                                                                                                               aCGTATAGCCTGATACTGGCGG‑TTATCTTTTTTT‑CTTTTT‑CTGGTGGGTTTCTG‑AAACGGGCG‑CCCTCCCCCTTTTTCCTTTCTTT‑AA‑GGGGGCCCAAAGGG‑AACTAAAAACAAAAAAACTTTTTAACACGGGGTGCggggggtt                                  >  1:11958/1‑141 (MQ=255)                                                                                                                          gATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATc                  <  1:471476/150‑1 (MQ=255)                                                                                                                                ggCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTaa           <  1:177717/151‑1 (MQ=255)                                                                                                                                ggCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTa            >  1:133086/1‑150 (MQ=255)                                                                                                                                  cGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTAAtt         <  1:17545/151‑1 (MQ=255)                                                                                                                                   gg‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTAAttt        >  2:539856/1‑151 (MQ=255)                                                                                                                                            ttATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTAATTTTCTGTc  <  1:708394/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                          CCCTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCA‑CTTTTA‑CGGATGGTTTCCTG‑AATCGGCTG‑CCATCCCGTTTCTGCCTGAC‑TT‑AA‑GGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTAATTTTCTGTC  >  NC_000913/2958631‑2958917

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑